npm - matsci-parse - Versions diffs - 0.16.3 → 0.16.4 - Mend

matsci-parse 0.16.3 → 0.16.4

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package/dist/__vite-browser-external-BApYF4Nn.js +9 -0
package/dist/__vite-browser-external-BApYF4Nn.js.map +1 -0
package/dist/index.js +1642 -1670
package/dist/index.js.map +1 -1
package/dist/rolldown-runtime-B0aSnxlc.js +20 -0
package/dist/stats.html +1 -1
package/package.json +1 -1

package/dist/index.js.map CHANGED Viewed

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{"version":3,"file":"index.js","names":["decodeEntities","parse"],"sources":["../lib/core/matrix/matrix.ts","../lib/core/math/constants.ts","../lib/core/math/numeric.ts","../lib/core/lattice/lattice.ts","../lib/core/matrix/operations/mul.ts","../lib/core/matrix/operations/inverse/inverse3x3.ts","../lib/core/matrix/operations/transpose.ts","../lib/core/structure/operations/applyTransformationBasis.ts","../lib/core/structure/operations/sortSites.ts","../lib/core/structure/operations/canonicalize.ts","../lib/core/structure/operations/hashStructure.ts","../lib/core/structure/operations/sites/appendSite.ts","../lib/core/structure/operations/sites/insertSite.ts","../lib/core/structure/operations/sites/removeSite.ts","../lib/core/structure/operations/sites/replaceSite.ts","../lib/core/matrix/operations/vector/cross.ts","../lib/core/matrix/operations/vector/norm.ts","../lib/core/matrix/operations/vector/normalize.ts","../lib/core/structure/operations/slab/reorientToNormal.ts","../lib/core/structure/operations/slab/addVacuum.ts","../lib/core/matrix/operations/lu.ts","../lib/core/matrix/operations/determinant.ts","../lib/core/matrix/operations/vector/dot.ts","../lib/core/lattice/inverse.ts","../lib/core/lattice/reciprocalLatticeCrystallographic.ts","../lib/core/structure/operations/slab/calculateScaleFactor.ts","../lib/core/site/cartesian.ts","../lib/core/site/fractional.ts","../lib/core/matrix/operations/latticePointsInSupercell.ts","../lib/core/structure/operations/supercell.ts","../lib/core/structure/operations/slab/slabFromMillerIndex.ts","../lib/core/structure/operations/distance/utils.ts","../lib/core/structure/operations/distance/getDisplacement.ts","../lib/core/lattice/reciprocalLattice.ts","../lib/core/structure/operations/geometry/plane.ts","../lib/core/structure/operations/slab/slabFromSites.ts","../lib/core/lattice/angles.ts","../lib/core/lattice/lengths.ts","../lib/core/lattice/metricTensor.ts","../lib/core/lattice/parameters.ts","../lib/core/lattice/kspacingToGrid.ts","../lib/core/lattice/create/fromParameters.ts","../lib/core/lattice/create/cubic.ts","../lib/core/lattice/create/hexagonal.ts","../lib/core/lattice/create/monoclinic.ts","../lib/core/lattice/create/orthorhombic.ts","../lib/core/lattice/create/rhombohedral.ts","../lib/core/lattice/create/tetragonal.ts","../lib/core/structure/operations/symmetry/spglib.ts","../lib/core/matrix/operations/scale.ts","../lib/core/matrix/operations/inverse/gaussJordan.ts","../lib/core/structure/operations/symmetry/brilliounzone/generateBZVertices.ts","../lib/core/structure/operations/symmetry/brilliounzone/bzPolyhedron.ts","../lib/core/structure/operations/symmetry/spgData.ts","../lib/core/matrix/operations/reduction/niggli.ts","../lib/core/structure/operations/symmetry/brilliounzone/seekpathTools.ts","../lib/core/structure/operations/symmetry/brilliounzone/bravais.ts","../lib/core/structure/operations/symmetry/brilliounzone/bandPathData.ts","../lib/core/structure/operations/symmetry/brilliounzone/seekpath.ts","../lib/core/structure/operations/symmetry/brilliounzone/bzVisualizerData.ts","../lib/core/data/periodictable/electronegativity.ts","../lib/core/structure/properties/formula.ts","../lib/core/structure/operations/symmetry/assign.ts","../lib/core/structure/operations/symmetry/matchStructures.ts","../lib/core/structure/operations/distance/getDistance.ts","../lib/core/structure/operations/distance/getDistances.ts","../lib/core/structure/operations/distance/getDistancesMatrix.ts","../lib/core/structure/operations/query/findSites.ts","../lib/core/structure/operations/query/findSitesBySpecies.ts","../lib/core/lattice/volume.ts","../lib/core/structure/properties/volume.ts","../lib/core/data/periodictable/atomicData.ts","../lib/core/structure/properties/cellMass.ts","../lib/core/structure/properties/density.ts","../lib/core/structure/properties/species.ts","../lib/core/site/site.ts","../lib/core/site/distance.ts","../lib/core/site/wrap.ts","../lib/core/species/species.ts","../lib/core/kpoints/index.ts","../lib/core/volumetric/volumetric.ts","../lib/core/volumetric/create/fill.ts","../lib/core/volumetric/create/fromFunction.ts","../lib/core/volumetric/create/fromMatrixSlices.ts","../lib/core/volumetric/create/ones.ts","../lib/core/volumetric/create/zeros.ts","../lib/core/io/cif/symmetryOperations.ts","../lib/core/io/helpers.ts","../lib/core/io/cif/index.ts","../lib/core/io/poscar.ts","../lib/core/io/structuredata.ts","../lib/core/io/xsf.ts","../lib/core/io/xyz.ts","../lib/core/io/optimade.ts","../lib/core/units/converter.ts","../lib/core/units/length.ts","../lib/core/io/gro.ts","../lib/core/io/pdb.ts","../lib/core/io/pw/ibrav.ts","../lib/core/io/pw/namelist.ts","../lib/core/io/pw/index.ts","../lib/core/io/kpoints/qe.ts","../lib/core/io/kpoints/vasp.ts","../lib/core/io/kpoints/crystal.ts","../lib/core/pseudopotential/pseudopotential.ts","../lib/core/io/pseudo/fortran-helpers.ts","../__vite-browser-external","../node_modules/.pnpm/txml@6.0.3/node_modules/txml/dist/index.mjs","../lib/core/io/pseudo/xml-helpers.ts","../lib/core/io/pseudo/upf.ts","../lib/core/io/pseudo/upf-v1.ts","../lib/core/units/energy.ts","../lib/core/units/angle.ts","../lib/core/pseudopotential/units.ts","../lib/core/io/pseudo/elements.ts","../lib/core/io/pseudo/fhi.ts","../lib/core/io/pseudo/psp8.ts","../lib/core/io/pseudo/psml.ts","../lib/core/pseudopotential/operations/listChannels.ts","../lib/core/pseudopotential/operations/getCutoffs.ts","../lib/core/pseudopotential/operations/makeRadialGrid.ts","../lib/core/pseudopotential/operations/resampleLinear.ts","../lib/core/pseudopotential/operations/kbToSemilocal.ts","../lib/core/pseudopotential/operations/semilocalToKb.ts","../lib/core/io/pseudo/gth.ts","../lib/core/io/pseudo/registry.ts","../lib/core/io/json.ts","../lib/core/io/ase.ts","../lib/core/io/pymatgen.ts","../lib/core/pseudopotential/validate.ts","../lib/core/data/symmetry/hallNumbers.ts","../lib/core/data/symmetry/pointGroups.ts"],"sourcesContent":["/** A matrix backed by a row-major Float64Array. /\nexport interface Matrix {\n readonly rows: number;\n readonly cols: number;\n readonly data: Float64Array;\n}\n\n/* Create a new Matrix with the given dimensions, optionally populated from an iterable.\n * @param rows - Number of rows.\n * @param cols - Number of columns.\n * @param data - Optional iterable of values to fill the matrix.\n * @returns A new Matrix. /\nexport function createMatrix(\n rows: number,\n cols: number,\n data?: Iterable<number>,\n): Matrix {\n const size = rows cols;\n\n const buffer = data ? Float64Array.from(data) : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(`Expected ${size} values, got ${buffer.length}`);\n }\n\n return {\n rows,\n cols,\n data: buffer,\n };\n}\n\n/** Return an identity matrix of the given size.\n * @param size - Number of rows and columns.\n * @returns A square identity matrix. /\nexport function identity(size: number): Matrix {\n const data = new Float64Array(size size);\n\n for (let i = 0; i < size; i++) {\n data[i * size + i] = 1;\n }\n\n return {\n rows: size,\n cols: size,\n data,\n };\n}\n\n/** Return a deep copy of the given matrix.\n * @param matrix - Matrix to clone.\n * @returns A new Matrix with copied data. /\nexport function clone(matrix: Matrix): Matrix {\n return {\n rows: matrix.rows,\n cols: matrix.cols,\n data: new Float64Array(matrix.data),\n };\n}\n\n/* Compute the linear index for the given (row, col) in a row-major layout.\n \n Useful for general matrix element access.\n * Performance-critical inner loops should generally use direct offset arithmetic.\n \n @param cols - Number of columns in the matrix.\n * @param row - Row index.\n * @param col - Column index.\n * @returns Linear index into the data array.\n /\nexport function index(cols: number, row: number, col: number): number {\n return row cols + col;\n}\n","/** Shared floating-point comparison threshold. /\nexport const EPSILON = 1e-12;\n","import { EPSILON } from \"./constants\";\n\n/* Zero-out values within EPSILON of zero. /\nexport function clean(x: number): number {\n return Math.abs(x) < EPSILON ? 0 : x;\n}\n\n/* Greatest common divisor. /\nexport function gcd(a: number, b: number): number {\n a = Math.abs(a);\n b = Math.abs(b);\n while (b !== 0) {\n [a, b] = [b, a % b];\n }\n return a;\n}\n\n/* Least common multiple. /\nexport function lcm(a: number, b: number): number {\n return (Math.abs(a) / gcd(a, b)) Math.abs(b);\n}\n","import { createMatrix, Matrix } from \"../matrix/matrix\";\nimport { clean } from \"../math/numeric\";\n\n/** A lattice defined by a 3x3 basis matrix (row vectors). /\nexport interface Lattice {\n basis: Matrix;\n}\n\n/* Create a Lattice from 3 diagonal lengths, 9 matrix values, or a Matrix. /\nexport function createLattice(\n data: number[] \| Float64Array \| Matrix \| [number, number, number],\n): Lattice {\n const values =\n data instanceof Float64Array\n ? Array.from(data)\n : \"data\" in data\n ? Array.from(data.data)\n : data;\n\n let m: Float64Array;\n\n if (values.length === 3) {\n const [a, b, c] = values;\n\n m = new Float64Array([a, 0, 0, 0, b, 0, 0, 0, c]);\n } else if (values.length === 9) {\n m = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n m[i] = clean(values[i]);\n }\n } else {\n throw new Error(\"Lattice requires 3 or 9 values\");\n }\n\n return {\n basis: createMatrix(3, 3, m),\n };\n}\n","import { Matrix, createMatrix } from \"../matrix\";\n\n/* Multiply two matrices (matrix product).\n * @param a - Left matrix.\n * @param b - Right matrix.\n * @returns A new Matrix containing the product. /\nexport function mul(a: Matrix, b: Matrix): Matrix {\n if (a.cols !== b.rows) {\n throw new Error(\"Invalid matrix multiplication dimensions\");\n }\n\n const out = createMatrix(a.rows, b.cols);\n\n const aRows = a.rows;\n const aCols = a.cols;\n const bCols = b.cols;\n\n const ad = a.data;\n const bd = b.data;\n const od = out.data;\n\n // Iterate row → k → col so B and the output are accessed sequentially\n // in their row-major layout, improving cache locality.\n for (let row = 0; row < aRows; row++) {\n const aOffset = row aCols;\n const outOffset = row * bCols;\n\n for (let k = 0; k < aCols; k++) {\n const aik = ad[aOffset + k];\n const bOffset = k * bCols;\n\n for (let col = 0; col < bCols; col++) {\n od[outOffset + col] += aik * bd[bOffset + col];\n }\n }\n }\n\n return out;\n}\n","import { Matrix, createMatrix } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a 3x3 matrix using cofactors.\n * @param m - A 3x3 matrix.\n * @returns The inverse Matrix. /\nexport function inverse3x3(m: Matrix): Matrix {\n if (m.rows !== 3 \|\| m.cols !== 3) {\n throw new Error(\"Expected 3x3 matrix\");\n }\n\n const a00 = m.data[0],\n a01 = m.data[1],\n a02 = m.data[2];\n const a10 = m.data[3],\n a11 = m.data[4],\n a12 = m.data[5];\n const a20 = m.data[6],\n a21 = m.data[7],\n a22 = m.data[8];\n\n const c00 = a11 a22 - a12 * a21;\n const c01 = a12 * a20 - a10 * a22;\n const c02 = a10 * a21 - a11 * a20;\n\n const c10 = a02 * a21 - a01 * a22;\n const c11 = a00 * a22 - a02 * a20;\n const c12 = a01 * a20 - a00 * a21;\n\n const c20 = a01 * a12 - a02 * a11;\n const c21 = a02 * a10 - a00 * a12;\n const c22 = a00 * a11 - a01 * a10;\n\n const det = a00 * c00 + a01 * c01 + a02 * c02;\n\n if (Math.abs(det) < EPSILON) {\n throw new Error(\"Singular matrix\");\n }\n\n const invDet = 1 / det;\n\n const out = createMatrix(3, 3);\n\n out.data[0] = c00 * invDet;\n out.data[1] = c10 * invDet;\n out.data[2] = c20 * invDet;\n\n out.data[3] = c01 * invDet;\n out.data[4] = c11 * invDet;\n out.data[5] = c21 * invDet;\n\n out.data[6] = c02 * invDet;\n out.data[7] = c12 * invDet;\n out.data[8] = c22 * invDet;\n\n return out;\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\n/** Transpose the given matrix (swap rows and columns).\n * @param matrix - Input matrix.\n * @returns A new transposed Matrix. /\nexport function transpose(matrix: Matrix): Matrix {\n const rows = matrix.rows;\n const cols = matrix.cols;\n\n const data = matrix.data;\n const out = createMatrix(cols, rows);\n const od = out.data;\n\n for (let row = 0; row < rows; row++) {\n const rowOffset = row cols;\n\n for (let col = 0; col < cols; col++) {\n od[col * rows + row] = data[rowOffset + col];\n }\n }\n\n return out;\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Site } from \"@/core/site/site\";\nimport type { Structure } from \"../structure\";\n\n/** Apply a transformation basis matrix to a structure.\n * The new lattice is P * oldBasis and fractional coordinates are P^{-T} * oldFrac,\n * preserving Cartesian positions.\n * @param structure - The input structure.\n * @param basis - A 3x3 transformation matrix.\n * @returns A new Structure with transformed lattice and sites. /\nexport function applyTransformationBasis(\n structure: Structure,\n basis: Matrix,\n): Structure {\n const invP = inverse3x3(basis);\n const newBasis = mul(basis, structure.lattice.basis);\n\n const sites: Site[] = structure.sites.map((site) => {\n const f = site.frac;\n const vec = {\n rows: 3,\n cols: 1,\n data: new Float64Array([f[0], f[1], f[2]]),\n };\n const result = mul(transpose(invP), vec);\n\n return {\n ...site,\n frac: new Float64Array([result.data[0], result.data[1], result.data[2]]),\n };\n });\n\n return {\n lattice: createLattice(newBasis),\n sites,\n };\n}\n","import { Site } from \"../../site/site\";\n\n/* Sort sites by species symbol, then by fractional coordinates (x, y, z). Returns a new array. /\nexport function sortSites(sites: Site[]): Site[] {\n return [...sites].sort((a, b) => {\n const sp = a.species.symbol.localeCompare(b.species.symbol);\n if (sp !== 0) return sp;\n if (a.frac[0] !== b.frac[0]) return a.frac[0] - b.frac[0];\n if (a.frac[1] !== b.frac[1]) return a.frac[1] - b.frac[1];\n return a.frac[2] - b.frac[2];\n });\n}\n","import { Structure } from \"../../structure/structure\";\nimport { sortSites } from \"./sortSites\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nfunction wrap(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < EPSILON ? 0 : v;\n}\n\n/* Return a copy with fractional coordinates wrapped to [0, 1), near-zero values cleaned, and sites sorted by species then coordinates. /\nexport function canonicalize(structure: Structure): Structure {\n const sites = structure.sites.map((site) => ({\n ...site,\n frac: new Float64Array([\n wrap(clean(site.frac[0])),\n wrap(clean(site.frac[1])),\n wrap(clean(site.frac[2])),\n ]),\n }));\n\n return { ...structure, sites: sortSites(sites) };\n}\n","import { Structure } from \"../structure\";\nimport { canonicalize } from \"./canonicalize\";\nimport { Vec3 } from \"../../site/site\";\n\nfunction toFixedArray(v: Vec3, precision = 8): string {\n return Array.from(v)\n .map((x) => x.toFixed(precision))\n .join(\",\");\n}\n\nfunction fnv1a(str: string): number {\n let hash = 2166136261;\n\n for (let i = 0; i < str.length; i++) {\n hash ^= str.charCodeAt(i);\n hash = 16777619;\n }\n\n return hash >>> 0;\n}\n\n/** FNV-1a hash of a canonicalized structure (lattice + sorted sites). /\nexport function hashStructure(structure: Structure): number {\n const s = canonicalize(structure);\n\n const lattice = s.lattice.basis.data;\n const latticeKey = toFixedArray(lattice);\n\n const sitesKey = s.sites\n .map((site) => {\n return site.species.symbol + \":\" + toFixedArray(site.frac);\n })\n .sort()\n .join(\"\|\");\n\n const key = latticeKey + \"::\" + sitesKey;\n\n return fnv1a(key);\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Append a single site to the structure. /\nexport function appendSite(structure: Structure, site: Site): Structure {\n const sites = structure.sites.slice();\n sites.push(site);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Append multiple sites to the structure. /\nexport function appendSites(\n structure: Structure,\n sitesToAppend: readonly Site[],\n): Structure {\n return {\n ...structure,\n sites: [...structure.sites, ...sitesToAppend],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Insert a single site at the given index. /\nexport function insertSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const oldSites = structure.sites;\n const sites = new Array(oldSites.length + 1);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n sites[index] = site;\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + 1] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Insert multiple sites starting at the given index. /\nexport function insertSites(\n structure: Structure,\n index: number,\n sitesToInsert: readonly Site[],\n): Structure {\n const oldSites = structure.sites;\n const n = sitesToInsert.length;\n\n const sites = new Array(oldSites.length + n);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n for (let i = 0; i < n; i++) {\n sites[index + i] = sitesToInsert[i];\n }\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + n] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Structure } from \"../../structure\";\n\n/* Remove the site at the given index. /\nexport function removeSite(structure: Structure, index: number): Structure {\n const sites = structure.sites.slice();\n sites.splice(index, 1);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Remove sites at the given indices. /\nexport function removeSites(\n structure: Structure,\n indices: readonly number[],\n): Structure {\n const remove = new Set(indices);\n\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => !remove.has(i)),\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Replace a single site at the given index. /\nexport function replaceSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const sites = structure.sites.slice();\n sites[index] = site;\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Replace multiple sites at the given indices. /\nexport function replaceSites(\n structure: Structure,\n replacements: readonly {\n index: number;\n site: Site;\n }[],\n): Structure {\n const sites = structure.sites.slice();\n\n for (const { index, site } of replacements) {\n sites[index] = site;\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Vector } from \"../../vector\";\n\n/* Compute the 3D cross product of two vectors.\n * @param a - First 3D vector.\n * @param b - Second 3D vector.\n * @returns The cross product vector. /\nexport function cross(a: Vector, b: Vector): Vector {\n if (a.length !== 3 \|\| b.length !== 3) {\n throw new Error(\"Cross product requires 3D vectors\");\n }\n\n return new Float64Array([\n a[1] b[2] - a[2] * b[1],\n a[2] * b[0] - a[0] * b[2],\n a[0] * b[1] - a[1] * b[0],\n ]);\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the Euclidean norm (magnitude) of a vector.\n * @param v - Input vector.\n * @returns The Euclidean norm. /\nexport function norm(v: Vector): number {\n let sum = 0;\n\n for (let i = 0; i < v.length; i++) {\n const x = v[i];\n sum += x x;\n }\n\n return Math.sqrt(sum);\n}\n","import { Vector } from \"../../vector\";\nimport { norm } from \"./norm\";\n\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Return a unit vector in the direction of v.\n * @param v - Input vector.\n * @returns A normalized unit vector. /\nexport function normalize(v: Vector): Vector {\n const n = norm(v);\n\n if (n < EPSILON) {\n throw new Error(\"Cannot normalize zero vector\");\n }\n\n const out = new Float64Array(v.length);\n\n for (let i = 0; i < v.length; i++) {\n out[i] = v[i] / n;\n }\n\n return out;\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { cross } from \"@/core/matrix/operations/vector/cross\";\nimport { normalize } from \"@/core/matrix/operations/vector/normalize\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/\n Rotate the lattice so that the given Cartesian direction maps to the new c-axis\n * (third lattice vector). Atom Cartesian positions are preserved exactly.\n \n NOTE: this only guarantees the new c-axis aligns with `normal` when the original\n * third lattice vector is parallel to `normal`. For slab construction, the caller\n * must first apply `calculateScaleFactor` + `supercell` to orient the cell.\n \n @param structure - The input structure.\n * @param normal - A 3D Cartesian direction vector (need not be unit).\n * @returns A new Structure with rotated lattice and sites.\n /\nexport function reorientToNormal(\n structure: Structure,\n normal: Float64Array \| number[],\n): Structure {\n const n = normalize(new Float64Array(normal));\n\n let e1: Float64Array;\n const ref = new Float64Array([1, 0, 0]);\n\n if (Math.abs(Math.abs(n[0]) - 1) < EPSILON) {\n e1 = normalize(cross(n, new Float64Array([0, 1, 0])));\n } else {\n e1 = normalize(cross(n, ref));\n }\n\n const e2 = cross(n, e1);\n\n const R = createMatrix(3, 3, [\n e1[0], e2[0], n[0],\n e1[1], e2[1], n[1],\n e1[2], e2[2], n[2],\n ]);\n\n return applyTransformationBasis(structure, R);\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/\n Add vacuum along the c-axis by stretching the c-vector.\n * Atom Cartesian positions are preserved exactly.\n * @param structure - The input structure (should already be reoriented with surface normal along c).\n * @param thickness - Vacuum thickness in the same length units as the lattice.\n * @returns A new Structure with extended c-vector.\n /\nexport function addVacuum(structure: Structure, thickness: number): Structure {\n if (thickness <= 0) return structure;\n\n const b = structure.lattice.basis.data;\n const cVec = new Float64Array([b[6], b[7], b[8]]);\n const cLength = norm(cVec);\n\n if (cLength < EPSILON) {\n throw new Error(\"c-vector has zero length\");\n }\n\n const scale = (cLength + thickness) / cLength;\n const P = createMatrix(3, 3, [1, 0, 0, 0, 1, 0, 0, 0, scale]);\n\n return applyTransformationBasis(structure, P);\n}\n","import { Matrix, clone } from \"../matrix\";\n\nimport { EPSILON } from \"../../math/constants\";\n\nexport interface LUDecomposition {\n readonly LU: Matrix;\n readonly piv: Int32Array;\n readonly sign: number;\n readonly singular: boolean;\n}\n\n/* Compute the LU decomposition of a square matrix with partial pivoting.\n * @param A - A square matrix.\n * @returns The LU decomposition. /\nexport function lu(A: Matrix): LUDecomposition {\n if (A.rows !== A.cols) {\n throw new Error(\"LU decomposition requires a square matrix\");\n }\n\n const n = A.rows;\n const LU = clone(A);\n const data = LU.data;\n const piv = new Int32Array(n);\n\n for (let i = 0; i < n; i++) {\n piv[i] = i;\n }\n\n let sign = 1;\n\n for (let k = 0; k < n; k++) {\n const rowK = k n;\n\n let pivot = k;\n let max = Math.abs(data[rowK + k]);\n\n // Find pivot row.\n for (let i = k + 1; i < n; i++) {\n const rowI = i * n;\n const v = Math.abs(data[rowI + k]);\n\n if (v > max) {\n max = v;\n pivot = i;\n }\n }\n\n if (max < EPSILON) {\n return {\n LU,\n piv,\n sign,\n singular: true,\n };\n }\n\n // Swap rows.\n if (pivot !== k) {\n const rowP = pivot * n;\n\n for (let j = 0; j < n; j++) {\n const tmp = data[rowK + j];\n data[rowK + j] = data[rowP + j];\n data[rowP + j] = tmp;\n }\n\n const tmp = piv[k];\n piv[k] = piv[pivot];\n piv[pivot] = tmp;\n\n sign = -sign;\n }\n\n const pivotVal = data[rowK + k];\n\n // Eliminate below pivot.\n for (let i = k + 1; i < n; i++) {\n const rowI = i * n;\n const factor = data[rowI + k] / pivotVal;\n\n data[rowI + k] = factor;\n\n for (let j = k + 1; j < n; j++) {\n data[rowI + j] -= factor * data[rowK + j];\n }\n }\n }\n\n return {\n LU,\n piv,\n sign,\n singular: false,\n };\n}\n","import { Matrix } from \"../matrix\";\nimport { lu } from \"./lu\";\n\n/** Compute the determinant of a square matrix using LU decomposition (O(n³)).\n * @param matrix - A square matrix.\n * @returns The determinant value. /\nexport function determinant(matrix: Matrix): number {\n if (matrix.rows !== matrix.cols) {\n throw new Error(\"Determinant requires a square matrix\");\n }\n\n const n = matrix.rows;\n\n // fast path for BZ / geometry\n if (n === 3) {\n const m = matrix.data;\n\n return (\n m[0] (m[4] * m[8] - m[5] * m[7]) -\n m[1] * (m[3] * m[8] - m[5] * m[6]) +\n m[2] * (m[3] * m[7] - m[4] * m[6])\n );\n }\n\n if (n === 1) {\n return matrix.data[0];\n }\n\n if (n === 2) {\n return matrix.data[0] * matrix.data[3] - matrix.data[1] * matrix.data[2];\n }\n\n const { LU, sign, singular } = lu(matrix);\n\n if (singular) return 0;\n\n const data = LU.data;\n let det = sign;\n\n for (let i = 0; i < n; i++) {\n det = data[i n + i];\n }\n\n return det;\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the dot product of two vectors.\n * @param a - First vector.\n * @param b - Second vector.\n * @returns The dot product. /\nexport function dot(a: Vector, b: Vector): number {\n if (a.length !== b.length) {\n throw new Error(\"Dot product requires same-length vectors\");\n }\n\n let sum = 0;\n\n for (let i = 0; i < a.length; i++) {\n sum += a[i] b[i];\n }\n\n return sum;\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse3x3 } from \"../matrix/operations/inverse/inverse3x3\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/** Compute the inverse of the lattice basis matrix. /\nexport function inverse(lattice: Lattice): Matrix {\n return inverse3x3(lattice.basis);\n}\n","import { Lattice, createLattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\n/* Compute the crystallographic reciprocal lattice (without 2pi scaling). /\nexport function reciprocalLatticeCrystallographic(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n return createLattice(invT.data);\n}\n","import { createMatrix, type Matrix } from \"@/core/matrix/matrix\";\nimport { determinant } from \"@/core/matrix/operations/determinant\";\nimport { dot } from \"@/core/matrix/operations/vector/dot\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport type { Lattice } from \"@/core/lattice/lattice\";\nimport { EPSILON } from \"@/core/math/constants\";\nimport { gcd, lcm } from \"@/core/math/numeric\";\n\nfunction reduceVector(v: number[]): number[] {\n let g = 0;\n for (const x of v) {\n g = gcd(g, Math.abs(Math.round(x)));\n }\n if (g <= 1) return v;\n return v.map((x) => Math.round(x / g));\n}\n\n/*\n Calculate the slab scale factor following pymatgen's `calculate_scaling_factor` algorithm.\n \n Given Miller indices (h, k, l), builds a 3×3 integer matrix U such that:\n * - Rows 0 and 1 are real-space vectors perpendicular to the surface normal (in-plane).\n * - Row 2 is a real-space vector with maximal projection onto the surface normal (c-direction).\n \n The key insight: a real-space vector v = r·lattice is perpendicular to the (hkl) surface\n * normal iff r·[h,k,l] = 0. In-plane rows are built as LCM combinations of lattice vectors\n * whose integer coefficients cancel the dot product with the Miller index.\n \n @param millerIndex - The Miller indices [h, k, l].\n * @param lattice - The crystal lattice.\n * @returns A 3×3 integer Matrix (the scale factor).\n /\nexport function calculateScaleFactor(\n millerIndex: [number, number, number],\n lattice: Lattice,\n): Matrix {\n const [h, k, l] = millerIndex;\n\n // Surface normal in Cartesian from reciprocal lattice\n const recip = reciprocalLatticeCrystallographic(lattice);\n const rb = recip.basis.data;\n const normalRaw = new Float64Array([\n h rb[0] + k * rb[3] + l * rb[6],\n h * rb[1] + k * rb[4] + l * rb[7],\n h * rb[2] + k * rb[5] + l * rb[8],\n ]);\n const normalLen = norm(normalRaw);\n if (normalLen < EPSILON) {\n throw new Error(\"Miller index [0,0,0] is invalid\");\n }\n const normal = new Float64Array(normalRaw.map((x) => x / normalLen));\n\n const basis = lattice.basis.data;\n const millerArr = [h, k, l];\n\n // Classify lattice vectors: in-plane (miller[i]==0) vs non-orthogonal\n const slabScaleFactor: number[][] = [];\n const nonOrthInd: [number, number][] = []; // [index, projection onto normal]\n\n for (let idx = 0; idx < 3; idx++) {\n if (millerArr[idx] === 0) {\n // Lattice vector is already in the surface plane\n const row = [0, 0, 0];\n row[idx] = 1;\n slabScaleFactor.push(row);\n } else {\n const aIdx = new Float64Array([\n basis[idx * 3],\n basis[idx * 3 + 1],\n basis[idx * 3 + 2],\n ]);\n const aLen = norm(aIdx);\n const d = Math.abs(dot(normal, aIdx)) / aLen;\n nonOrthInd.push([idx, d]);\n }\n }\n\n // Pick the vector with maximum projection onto normal as the c-direction\n let cIndex = nonOrthInd[0][0];\n let maxProj = nonOrthInd[0][1];\n for (const [idx, proj] of nonOrthInd) {\n if (proj > maxProj) {\n cIndex = idx;\n maxProj = proj;\n }\n }\n\n // Build in-plane vectors from non-orthogonal pairs using LCM combinations\n // For pair (ii, jj): row[ii] = -lcm/m[ii], row[jj] = lcm/m[jj]\n // This ensures row·[h,k,l] = (-lcm/m[ii])m[ii] + (lcm/m[jj])m[jj] = -lcm + lcm = 0\n if (nonOrthInd.length > 1) {\n const millerNonZero = nonOrthInd.map(([idx]) => Math.abs(millerArr[idx]));\n let lcmVal = millerNonZero[0];\n for (let i = 1; i < millerNonZero.length; i++) {\n lcmVal = lcm(lcmVal, millerNonZero[i]);\n }\n\n for (let ii = 0; ii < nonOrthInd.length; ii++) {\n for (let jj = ii + 1; jj < nonOrthInd.length; jj++) {\n const iiIdx = nonOrthInd[ii][0];\n const jjIdx = nonOrthInd[jj][0];\n const row = [0, 0, 0];\n row[iiIdx] = -Math.round(lcmVal / millerArr[iiIdx]);\n row[jjIdx] = Math.round(lcmVal / millerArr[jjIdx]);\n slabScaleFactor.push(reduceVector(row));\n if (slabScaleFactor.length === 2) break;\n }\n if (slabScaleFactor.length === 2) break;\n }\n }\n\n // Add c-direction vector: use the lattice vector at cIndex (identity row)\n const cRow = [0, 0, 0];\n cRow[cIndex] = 1;\n slabScaleFactor.push(cRow);\n\n // Build matrix\n const flat = slabScaleFactor.flat();\n let mat = createMatrix(3, 3, flat);\n\n // Ensure positive determinant (left-handed → negate first row)\n if (determinant(mat) < 0) {\n mat = createMatrix(\n 3,\n 3,\n flat.map((x, i) => (i < 3 ? -x : x)),\n );\n }\n\n return mat;\n}\n","import { mul } from \"../matrix/operations/mul\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nimport { Site } from \"./site\";\nimport { Lattice } from \"../lattice/lattice\";\nimport { Vector } from \"../matrix/vector\";\n\n/** Convert a site's fractional coordinates to Cartesian.\n * @param lattice - The lattice.\n * @param site - The site.\n * @returns Cartesian coordinate vector. /\nexport function cartesian(lattice: Lattice, site: Site): Vector {\n const [x, y, z] = site.frac;\n\n const frac = {\n rows: 3,\n cols: 1,\n data: new Float64Array([x, y, z]),\n };\n\n const basisT = transpose(lattice.basis);\n const result = mul(basisT, frac);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { inverse } from \"../lattice/inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Vector } from \"../matrix/vector\";\nimport { Lattice } from \"../lattice/lattice\";\n\n/* Convert Cartesian coordinates to fractional.\n * @param lattice - The lattice.\n * @param cart - Cartesian vector.\n * @returns Fractional coordinate vector. /\nexport function fractional(lattice: Lattice, cart: Vector): Vector {\n const vec = {\n rows: 3,\n cols: 1,\n data: cart,\n };\n\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const result = mul(invT, vec);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { Matrix, createMatrix } from \"../matrix\";\nimport { inverse3x3 } from \"./inverse/inverse3x3\";\n\n/\n Return fractional coordinates (in the original cell) of all lattice points\n * that lie inside the supercell defined by an integer transformation matrix U.\n \n The new cell has basis B' = U @ B. A lattice point at integer vector n\n * maps to fractional coordinate inv(U) @ n in the original cell. We collect\n * all n such that inv(U) @ n has every component in [0, 1).\n \n The number of returned points equals \|det(U)\|.\n \n @param U - A 3×3 integer transformation matrix.\n * @returns An array of 3-element Float64Arrays, each a fractional coordinate.\n /\nexport function latticePointsInSupercell(U: Matrix): Float64Array[] {\n const invU = inverse3x3(U);\n\n // Determine search range: entries of inv(U) scale the integer vectors,\n // so we need to cover enough range. For typical slab scale factors\n // (entries 0, ±1, ±2), ±4 is ample.\n const maxEntry = Math.max(\n ...Array.from(U.data).map(Math.abs),\n 1,\n );\n const range = maxEntry + 2;\n\n const points: Float64Array[] = [];\n\n for (let i = -range; i <= range; i++) {\n for (let j = -range; j <= range; j++) {\n for (let k = -range; k <= range; k++) {\n // frac = invU @ [i, j, k]\n const d = invU.data;\n const f0 = d[0] i + d[1] * j + d[2] * k;\n const f1 = d[3] * i + d[4] * j + d[5] * k;\n const f2 = d[6] * i + d[7] * j + d[8] * k;\n\n if (\n f0 >= -1e-10 && f0 < 1 - 1e-10 &&\n f1 >= -1e-10 && f1 < 1 - 1e-10 &&\n f2 >= -1e-10 && f2 < 1 - 1e-10\n ) {\n points.push(\n new Float64Array([\n Math.max(0, f0),\n Math.max(0, f1),\n Math.max(0, f2),\n ]),\n );\n }\n }\n }\n }\n\n return points;\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { cartesian } from \"@/core/site/cartesian\";\nimport { fractional } from \"@/core/site/fractional\";\nimport { latticePointsInSupercell } from \"@/core/matrix/operations/latticePointsInSupercell\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Structure } from \"../structure\";\nimport type { Site } from \"@/core/site/site\";\n\ntype SupercellSize = number \| [number, number, number] \| Matrix;\n\nfunction isMatrix(size: SupercellSize): size is Matrix {\n return typeof size !== \"number\" && !Array.isArray(size);\n}\n\n/** Create a supercell by applying an integer transformation matrix U.\n \n If `size` is a number or [nx, ny, nz], a diagonal supercell is formed by\n * replicating the structure in each lattice direction.\n \n If `size` is a 3x3 integer Matrix, the general supercell algorithm from\n * pymatgen's `Structure.__mul__` (make_supercell) is used: the new basis\n * is U @ oldBasis and lattice points are replicated by \|det(U)\|.\n \n @param structure - The input structure.\n * @param size - Supercell size: number (isotropic), [nx, ny, nz], or 3x3 integer matrix.\n * @returns A new Structure with the supercell applied.\n /\nexport function supercell(structure: Structure, size: SupercellSize): Structure {\n let U: Matrix;\n\n if (isMatrix(size)) {\n U = size;\n } else {\n const [nx, ny, nz] = typeof size === \"number\" ? [size, size, size] : size;\n U = createMatrix(3, 3, [nx, 0, 0, 0, ny, 0, 0, 0, nz]);\n }\n\n const newBasis = mul(U, structure.lattice.basis);\n const newLattice = createLattice(newBasis);\n\n const fracPoints = latticePointsInSupercell(U);\n\n const sites: Site[] = [];\n\n for (const site of structure.sites) {\n const siteCart = cartesian(structure.lattice, site);\n\n for (const lp of fracPoints) {\n // Lattice point in Cartesian (using new lattice)\n const lpCart = cartesian(newLattice, {\n species: site.species,\n frac: lp,\n });\n\n const pos = new Float64Array([\n siteCart[0] + lpCart[0],\n siteCart[1] + lpCart[1],\n siteCart[2] + lpCart[2],\n ]);\n\n const frac = fractional(newLattice, pos);\n\n // Wrap to [0, 1)\n for (let d = 0; d < 3; d++) {\n frac[d] = frac[d] - Math.floor(frac[d]);\n if (frac[d] > 1 - 1e-10) frac[d] = 0;\n if (frac[d] < 1e-10) frac[d] = 0;\n }\n\n sites.push({\n species: site.species,\n frac,\n });\n }\n }\n\n return {\n lattice: newLattice,\n sites,\n };\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { calculateScaleFactor } from \"./calculateScaleFactor\";\nimport { supercell } from \"../supercell\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /* Number of unit cell replications along c (surface normal). Default 1. /\n layers?: number;\n /* Vacuum thickness in Angstroms. Default 0. /\n vacuum?: number;\n}\n\n/\n Generate a slab oriented along the (hkl) plane, following pymatgen's algorithm.\n \n Steps:\n * 1. Calculate an integer scale factor U that puts in-plane vectors perpendicular\n * to the surface normal, and a c-vector with max projection onto the normal.\n * 2. Apply make_supercell(U) to create an oriented unit cell (OUC).\n * 3. Replicate the OUC along c to get the desired number of layers.\n * 4. Add vacuum by stretching the c-vector.\n \n @param structure - The bulk input structure.\n * @param h - Miller index h.\n * @param k - Miller index k.\n * @param l - Miller index l.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n /\nexport function slabFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n // Step 1: Calculate the scale factor\n const U = calculateScaleFactor([h, k, l], structure.lattice);\n\n // Step 2: Create the oriented unit cell\n const ouc = supercell(structure, U);\n\n // Step 3: Replicate along c\n const replicated = supercell(ouc, [1, 1, layers]);\n\n // Step 4: Add vacuum\n return addVacuum(replicated, vacuum);\n}\n","/* A 3-component vector. /\nexport type Vec3 = Float64Array;\n\n// TODO: these are sort of generic geomtery utils\n// perhaps they would be better served higher up.\n\n/* Wrap a fractional displacement into the minimum-image convention (components in [-0.5, 0.5]). /\nexport function minimumImage(df: Vec3): Float64Array {\n return new Float64Array([\n df[0] - Math.round(df[0]),\n df[1] - Math.round(df[1]),\n df[2] - Math.round(df[2]),\n ]);\n}\n/* Squared distance from a minimum-image vector using the metric tensor G. /\nexport function distanceSquared(mic: Vec3, G: Float64Array): number {\n const x = mic[0],\n y = mic[1],\n z = mic[2];\n\n return (\n x (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z)\n );\n}\n","import { Structure } from \"../../structure\";\nimport { minimumImage } from \"./utils\";\n/** A 3-component vector. /\nexport type Vec3 = Float64Array;\n\n/* Minimum-image displacement vector from site idx1 to site idx2. /\nexport function getDisplacement(\n structure: Structure,\n idx1: number,\n idx2: number,\n): Vec3 {\n const s1 = structure.sites[idx1];\n const s2 = structure.sites[idx2];\n\n return minimumImage([\n s2.frac[0] - s1.frac[0],\n s2.frac[1] - s1.frac[1],\n s2.frac[2] - s1.frac[2],\n ]);\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { createLattice } from \"./lattice\";\n\nconst TWO_PI = 2 Math.PI;\n\n/** Compute the reciprocal lattice scaled by 2pi. /\nexport function reciprocalLattice(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const data = invT.data.map((v) => v * TWO_PI);\n\n return createLattice(data);\n}\n","import { Structure } from \"../../structure\";\nimport { getDisplacement } from \"../distance/getDisplacement\";\nimport { cross } from \"../../../matrix/operations/vector/cross\";\nimport { norm } from \"../../../matrix/operations/vector/norm\";\nimport { cartesian } from \"../../../site/cartesian\";\n\nimport { reciprocalLattice } from \"../../../lattice/reciprocalLattice\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** A plane defined by a unit normal and a point on the plane (Cartesian). /\nexport interface Plane {\n readonly normal: Float64Array;\n readonly point: Float64Array;\n}\n\n/* Plane equation in the form ax + by + cz + d = 0. /\nexport interface PlaneEquation {\n readonly a: number;\n readonly b: number;\n readonly c: number;\n readonly d: number;\n}\n\n/* Plane through three non-collinear sites. /\nexport function planeFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n): Plane {\n // Cartesian displacement vectors\n const r1 = getDisplacement(structure, i, j);\n const r2 = getDisplacement(structure, i, k);\n\n const n = cross(r1, r2);\n const nNorm = norm(n);\n\n if (nNorm < EPSILON) {\n throw new Error(\"Cannot construct plane from collinear sites\");\n }\n\n const normal = new Float64Array([n[0] / nNorm, n[1] / nNorm, n[2] / nNorm]);\n\n // pick a real point on plane (site i), convert properly\n const point = cartesian(structure.lattice, structure.sites[i]);\n\n return { normal, point };\n}\n\n/* Convert a Plane to PlaneEquation coefficients (ax + by + cz + d = 0). /\nexport function planeEquation(plane: Plane): PlaneEquation {\n const { normal, point } = plane;\n\n const d = -(\n normal[0] point[0] +\n normal[1] * point[1] +\n normal[2] * point[2]\n );\n\n return {\n a: normal[0],\n b: normal[1],\n c: normal[2],\n d,\n };\n}\n\n/** Signed distance from a Cartesian point to a plane. /\nexport function distanceFromPlane(\n point: Float64Array,\n plane: PlaneEquation,\n): number {\n const { a, b, c, d } = plane;\n\n const denominator = Math.sqrt(a a + b * b + c * c);\n\n if (denominator < EPSILON) {\n throw new Error(\"Invalid plane normal\");\n }\n\n return (a * point[0] + b * point[1] + c * point[2] + d) / denominator;\n}\n\n/** Signed distance from a site to a plane. /\nexport function distanceFromSiteToPlane(\n structure: Structure,\n siteIndex: number,\n plane: PlaneEquation,\n): number {\n const point = cartesian(structure.lattice, structure.sites[siteIndex]);\n\n return distanceFromPlane(point, plane);\n}\n\n/* Plane from Miller indices (hkl) using the reciprocal lattice. /\nexport function planeFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n): Plane {\n const reciprocal = reciprocalLattice(structure.lattice);\n\n const normal = new Float64Array([\n h reciprocal.basis.data[0] +\n k * reciprocal.basis.data[3] +\n l * reciprocal.basis.data[6],\n\n h * reciprocal.basis.data[1] +\n k * reciprocal.basis.data[4] +\n l * reciprocal.basis.data[7],\n\n h * reciprocal.basis.data[2] +\n k * reciprocal.basis.data[5] +\n l * reciprocal.basis.data[8],\n ]);\n\n const length = norm(normal);\n\n if (length < EPSILON) {\n throw new Error(\"Invalid Miller index\");\n }\n\n return {\n normal: new Float64Array([\n normal[0] / length,\n normal[1] / length,\n normal[2] / length,\n ]),\n point: new Float64Array([0, 0, 0]),\n };\n}\n","import { planeFromSites } from \"../geometry/plane\";\nimport { canonicalize } from \"../canonicalize\";\nimport { supercell } from \"../supercell\";\nimport { reorientToNormal } from \"./reorientToNormal\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /** Number of unit cell replications along c (surface normal). Default 1. /\n layers?: number;\n /* Vacuum thickness in lattice length units. Default 0. /\n vacuum?: number;\n}\n\n/\n Generate a slab oriented so the plane through three sites is the surface.\n \n Steps: plane normal → rotation → replicate → add vacuum.\n * Atom Cartesian positions within the slab are preserved exactly.\n \n @param structure - The bulk input structure.\n * @param i - Index of first site defining the surface plane.\n * @param j - Index of second site defining the surface plane.\n * @param k - Index of third site defining the surface plane.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n /\nexport function slabFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n const plane = planeFromSites(structure, i, j, k);\n const reoriented = canonicalize(reorientToNormal(structure, plane.normal));\n const replicated = supercell(reoriented, [1, 1, layers]);\n\n return addVacuum(replicated, vacuum);\n}\n","import { dot } from \"../matrix/operations/vector/dot\";\nimport { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n\nimport { Vector } from \"../matrix/vector\";\n\nfunction angle(u: Vector, v: Vector) {\n const denom = norm(u) norm(v);\n if (Math.abs(denom) < 1e-300) throw new Error(\"Zero-length lattice vector\");\n\n const c = dot(u, v) / denom;\n const clamped = Math.max(-1, Math.min(1, c));\n\n return Math.acos(clamped);\n}\n\n/** Compute the three inter-vector angles (alpha, beta, gamma) in radians. /\nexport function angles(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Vector = new Float64Array([m[0], m[1], m[2]]);\n const b: Vector = new Float64Array([m[3], m[4], m[5]]);\n const c: Vector = new Float64Array([m[6], m[7], m[8]]);\n\n const alpha = angle(b, c);\n const beta = angle(a, c);\n const gamma = angle(a, b);\n\n return [alpha, beta, gamma];\n}\n","import { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n/* Compute the three lattice vector lengths (a, b, c). /\nexport function lengths(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Float64Array = new Float64Array([m[0], m[1], m[2]]);\n const b: Float64Array = new Float64Array([m[3], m[4], m[5]]);\n const c: Float64Array = new Float64Array([m[6], m[7], m[8]]);\n\n return [norm(a), norm(b), norm(c)];\n}\n","import { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Lattice } from \"./lattice\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/* Compute the metric tensor G = A A^T for the lattice basis (row vectors). /\nexport function metricTensor(lattice: Lattice): Matrix {\n const A = lattice.basis;\n\n const AT = transpose(A);\n return mul(A, AT);\n}\n","import { lengths } from \"./lengths\";\nimport { angles } from \"./angles\";\nimport { Lattice } from \"./lattice\";\n\nconst RAD2DEG = 180 / Math.PI;\n\n/* Return lattice parameters (a, b, c, alpha, beta, gamma) with angles in degrees. /\nexport function parameters(\n lattice: Lattice,\n): [number, number, number, number, number, number] {\n const [a, b, c] = lengths(lattice);\n const [alpha, beta, gamma] = angles(lattice);\n\n return [a, b, c, alpha RAD2DEG, beta * RAD2DEG, gamma * RAD2DEG];\n}\n","import { Lattice } from \"./lattice\";\nimport { reciprocalLatticeCrystallographic } from \"./reciprocalLatticeCrystallographic\";\nimport { lengths } from \"./lengths\";\n\n/** Compute k-point grid [Nx, Ny, Nz] from desired spacing in Å⁻¹. /\nexport function kspacingToGrid(\n lattice: Lattice,\n spacing: number,\n): [number, number, number] {\n if (spacing <= 0) {\n throw new Error(\"k-spacing must be positive\");\n }\n\n const rec = reciprocalLatticeCrystallographic(lattice);\n const [b1, b2, b3] = lengths(rec);\n\n return [\n Math.max(1, Math.ceil((b1 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b2 * 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b3 * 2 * Math.PI) / spacing)),\n ];\n}\n","import { createLattice } from \"../lattice\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nconst DEG2RAD = Math.PI / 180;\n\n/** Create a Lattice from conventional cell parameters (angles in degrees). /\nexport function fromParameters(\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n) {\n const alphaR = alpha DEG2RAD;\n const betaR = beta * DEG2RAD;\n const gammaR = gamma * DEG2RAD;\n\n const cosA = Math.cos(alphaR);\n const cosB = Math.cos(betaR);\n const cosG = Math.cos(gammaR);\n const sinG = Math.sin(gammaR);\n\n // lattice vectors\n const v1 = [a, 0, 0];\n\n const v2 = [b * cosG, b * sinG, 0];\n\n // guard against degenerate gamma\n if (Math.abs(sinG) < EPSILON) {\n throw new Error(\"Invalid lattice: gamma too close to 0 or 180 degrees\");\n }\n\n const cx = c * cosB;\n\n const cy = (c * (cosA - cosB * cosG)) / sinG;\n\n const czSquared = c * c - cx * cx - cy * cy;\n\n const cz = Math.sqrt(Math.max(0, czSquared));\n\n return createLattice([\n clean(v1[0]),\n clean(v1[1]),\n clean(v1[2]),\n clean(v2[0]),\n clean(v2[1]),\n clean(v2[2]),\n clean(cx),\n clean(cy),\n clean(cz),\n ]);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/** Create a cubic lattice with side length a. /\nexport function cubic(a: number) {\n return fromParameters(a, a, a, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a hexagonal lattice with side a and height c. /\nexport function hexagonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 120);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a monoclinic lattice (alpha=gamma=90, beta given in degrees). /\nexport function monoclinic(a: number, b: number, c: number, beta: number) {\n return fromParameters(a, b, c, 90, beta, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create an orthorhombic lattice with sides a, b, c and all angles 90. /\nexport function orthorhombic(a: number, b: number, c: number) {\n return fromParameters(a, b, c, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a rhombohedral lattice with side a and equal angles alpha (degrees). /\nexport function rhombohedral(a: number, alpha: number) {\n return fromParameters(a, a, a, alpha, alpha, alpha);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a tetragonal lattice with a=b, c, and all angles 90. /\nexport function tetragonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 90);\n}\n","/\n First-class symmetry engine backed by `@spglib/moyo-wasm`.\n \n This is the primary way to run structure-symmetry analysis in the library.\n * All `analyze_cell`/space-group work goes through the moyo WASM module here.\n * (The lattice Niggli reduction that seekpath used to obtain from the legacy\n * `spglib-wasm/` hand-rolled build is now a pure-TS implementation in\n * `matrix/operations/reduction/niggli.ts`.)\n \n `analyze_cell` is synchronous once the WASM is loaded; the async wrappers\n * below exist to await the one-time `init()` and keep the public API uniform.\n /\n\nimport init, { analyze_cell } from \"@spglib/moyo-wasm\";\nimport type { MoyoDataset } from \"@spglib/moyo-wasm\";\n\nimport { createLattice } from \"@/core/lattice\";\nimport { Structure } from \"../../structure\";\n\nlet ready: Promise<unknown> \| null = null;\n\n/* Ensure the Moyo WASM module is loaded (idempotent). /\nexport function initMoyo() {\n if (!ready) {\n ready = (async () => {\n try {\n // In Node.js (tests) read the wasm bytes from disk; the browser fetches\n // the URL that the package resolves for itself.\n if (typeof process !== \"undefined\" && process.versions?.node) {\n const { readFileSync } = await import(\"fs\");\n const { createRequire } = await import(\"module\");\n const require = createRequire(import.meta.url);\n const wasmPath = require.resolve(\n \"@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n );\n return await init({ module_or_path: readFileSync(wasmPath) });\n }\n return await init();\n } catch (e) {\n // Don't cache rejections: allow a later call to retry the load.\n ready = null;\n throw e;\n }\n })();\n }\n return ready;\n}\n\n/* Serialize a structure into the Moyo/SPGLIB input representation. /\nfunction toMoyoInput(structure: Structure): {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n} {\n const symbolToId = new Map<string, number>();\n const numbers: number[] = [];\n const positions: number[][] = [];\n\n let counter = 0;\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n counter++;\n }\n\n positions.push(Array.from(site.frac));\n numbers.push(symbolToId.get(symbol)!);\n }\n\n return {\n lattice: { basis: Array.from(structure.lattice.basis.data) },\n positions,\n numbers,\n };\n}\n\n/* Run the symmetry engine on a structure and return the raw Moyo dataset. /\nexport async function analyzeStructure(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Spglib\",\n): Promise<MoyoDataset> {\n await initMoyo();\n return analyze_cell(\n JSON.stringify(toMoyoInput(structure)),\n tolerance,\n setting,\n );\n}\n\n/* Compute primitive and conventional structures plus calculation results via Moyo/SPGLIB. /\nexport async function getSymmetry(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Spglib\",\n): Promise<{\n primitive: Structure;\n conventional: Structure;\n calculationResults: MoyoDataset;\n}> {\n await initMoyo();\n\n // -----------------------------\n // 1. Run symmetry engine\n // -----------------------------\n const results = await analyzeStructure(structure, tolerance, setting);\n\n // -----------------------------\n // 2. Build reversible mapping\n // -----------------------------\n const symbolToId = new Map<string, number>();\n const idToSymbol = new Map<number, string>();\n\n {\n let counter = 0;\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n idToSymbol.set(counter, symbol);\n counter++;\n }\n }\n }\n\n function build(cell: {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n }): Structure {\n const { lattice, positions, numbers } = cell;\n\n const species = [...new Set(numbers)].map((n: number) => ({\n symbol: idToSymbol.get(n)!,\n }));\n\n const sites = positions.map((pos: number[], i: number) => ({\n species: {\n symbol: idToSymbol.get(numbers[i])!,\n },\n frac: new Float64Array(pos),\n }));\n\n return {\n lattice: createLattice(lattice.basis),\n species,\n sites,\n };\n }\n\n // -----------------------------\n // 3. Return both structures\n // -----------------------------\n return {\n primitive: build(results.prim_std_cell),\n conventional: build(results.std_cell),\n calculationResults: results,\n };\n}\n","import { Matrix, createMatrix } from \"../matrix\";\n\n/* Multiply every element of matrix m by scalar k.\n * @param m - Input matrix.\n * @param k - Scalar multiplier.\n * @returns A new scaled Matrix. /\nexport function scale(m: Matrix, k: number): Matrix {\n const out = createMatrix(m.rows, m.cols);\n\n const size = m.data.length;\n\n for (let i = 0; i < size; i++) {\n out.data[i] = m.data[i] k;\n }\n\n return out;\n}\n","import { Matrix, createMatrix, clone, index } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a square matrix using Gauss-Jordan elimination with partial pivoting.\n * @param m - A square matrix.\n * @returns The inverse Matrix. /\nexport function gjInverse(m: Matrix): Matrix {\n if (m.rows !== m.cols) {\n throw new Error(\"Inverse requires square matrix\");\n }\n\n const n = m.rows;\n const A = clone(m);\n const I = createMatrix(n, n);\n const Adata = A.data;\n const Idata = I.data;\n\n // Initialize identity\n for (let i = 0; i < n; i++) {\n Idata[i n + i] = 1;\n }\n\n for (let i = 0; i < n; i++) {\n let pivotIdx = i * n + i;\n\n // Pivoting\n if (Math.abs(Adata[pivotIdx]) < EPSILON) {\n let swapRow = -1;\n for (let r = i + 1; r < n; r++) {\n if (Math.abs(Adata[r * n + i]) > EPSILON) {\n swapRow = r;\n break;\n }\n }\n if (swapRow === -1) {\n throw new Error(\"Singular matrix\");\n }\n\n // performant inline swap\n const r1Offset = i * n;\n const r2Offset = swapRow * n;\n for (let c = 0; c < n; c++) {\n let tmp = Adata[r1Offset + c];\n Adata[r1Offset + c] = Adata[r2Offset + c];\n Adata[r2Offset + c] = tmp;\n\n tmp = Idata[r1Offset + c];\n Idata[r1Offset + c] = Idata[r2Offset + c];\n Idata[r2Offset + c] = tmp;\n }\n\n pivotIdx = i * n + i;\n }\n\n const pivot = Adata[pivotIdx];\n const invPivot = 1 / pivot;\n\n // Normalize pivot row\n const pivotOffset = i * n;\n for (let c = 0; c < n; c++) {\n Adata[pivotOffset + c] = invPivot;\n Idata[pivotOffset + c] = invPivot;\n }\n\n // Eliminate other rows\n for (let r = 0; r < n; r++) {\n if (r === i) continue;\n\n const factor = Adata[r * n + i];\n if (Math.abs(factor) < EPSILON) continue;\n\n const rOffset = r * n;\n for (let c = 0; c < n; c++) {\n Adata[rOffset + c] -= Adata[pivotOffset + c] * factor;\n Idata[rOffset + c] -= Idata[pivotOffset + c] * factor;\n }\n }\n }\n\n return I;\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { Structure } from \"@/core/structure/structure\";\nimport { dot, mul } from \"@/core/matrix/operations\";\n\nimport { determinant } from \"@/core/matrix/operations\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { Vector } from \"@/core/matrix/vector\";\n\ninterface Plane {\n normal: Float64Array;\n offset: number;\n}\n\nfunction intersectPlanes(\n p1: Plane,\n p2: Plane,\n p3: Plane,\n tolerance = 1e-10,\n): Float64Array \| null {\n const A = createMatrix(3, 3, [...p1.normal, ...p2.normal, ...p3.normal]);\n\n const detA = determinant(A);\n\n if (Math.abs(detA) < tolerance) return null;\n\n const invA = inverse3x3(A);\n\n const d = createMatrix(3, 1, [p1.offset, p2.offset, p3.offset]);\n\n const res = mul(invA, d).data;\n\n return new Float64Array([res[0], res[1], res[2]]);\n}\n\nfunction key(v: Float64Array) {\n const nx = v[0],\n ny = v[1],\n nz = v[2];\n const inv = 1 / Math.sqrt(nx * nx + ny * ny + nz * nz);\n\n // normalize direction so ±G collapse\n const x = Math.round(nx * inv * 1e6);\n const y = Math.round(ny * inv * 1e6);\n const z = Math.round(nz * inv * 1e6);\n\n return `${x},${y},${z}`;\n}\n\nfunction vkey(v: Float64Array, eps = 1e-6) {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\nfunction isInside(v: Float64Array, planes: Plane[]) {\n const tolerance = 0.0;\n for (const p of planes) {\n const d = p.normal[0] * v[0] + p.normal[1] * v[1] + p.normal[2] * v[2];\n\n if (d > p.offset + tolerance) return false;\n }\n return true;\n}\n\n/** Generate Brillouin zone vertices from the reciprocal crystallographic lattice. /\nexport async function generateBZVertices(\n structure: Structure,\n tolerance: number = 1e-4,\n): Promise<Float64Array[]> {\n const reciprocalLattice = reciprocalLatticeCrystallographic(\n structure.lattice,\n );\n\n const rcLD = reciprocalLattice.basis.data;\n\n const aStar = [rcLD[0], rcLD[1], rcLD[2]];\n const bStar = [rcLD[3], rcLD[4], rcLD[5]];\n const cStar = [rcLD[6], rcLD[7], rcLD[8]];\n\n const range = 2;\n const points: Vector[] = [];\n\n for (let h = -range; h <= range; h++) {\n for (let k = -range; k <= range; k++) {\n for (let l = -range; l <= range; l++) {\n const point = new Float64Array(3);\n\n point[0] = h aStar[0] + k * bStar[0] + l * cStar[0];\n\n point[1] = h * aStar[1] + k * bStar[1] + l * cStar[1];\n\n point[2] = h * aStar[2] + k * bStar[2] + l * cStar[2];\n\n points.push(point);\n }\n }\n }\n\n // remove center point\n const neighbors = points.filter(\n (p) =>\n Math.abs(p[0]) > tolerance \|\|\n Math.abs(p[1]) > tolerance \|\|\n Math.abs(p[2]) > tolerance,\n );\n\n // sort by distance from origin\n neighbors.sort((a, b) => {\n const da = a[0] * a[0] + a[1] * a[1] + a[2] * a[2];\n\n const db = b[0] * b[0] + b[1] * b[1] + b[2] * b[2];\n\n return da - db;\n });\n\n const map = new Map<string, Float64Array>();\n\n for (const p of neighbors) {\n const k = key(p);\n if (!map.has(k)) map.set(k, p);\n }\n\n const uniqueNeighbors = [...map.values()];\n\n // console.log(uniqueNeighbors); // all neighbor recip points\n\n const planes = uniqueNeighbors.slice(0, 26).map((G) => ({\n normal: G,\n offset: dot(G, G) / 2,\n }));\n\n const candidateBZCorners: Float64Array[] = [];\n\n for (let i = 0; i < planes.length; i++) {\n for (let j = i + 1; j < planes.length; j++) {\n for (let k = j + 1; k < planes.length; k++) {\n const v = intersectPlanes(planes[i], planes[j], planes[k], tolerance);\n\n if (!v) continue;\n\n if (isInside(v, planes)) {\n candidateBZCorners.push(v);\n }\n }\n }\n }\n\n const vertexMap = new Map<string, Float64Array>();\n\n for (const v of candidateBZCorners) {\n const k = vkey(v);\n if (!vertexMap.has(k)) {\n vertexMap.set(k, v);\n }\n }\n\n const hullVertices = [...vertexMap.values()];\n\n return hullVertices;\n}\n","/*\n Compute the triangulated polyhedron of the first Brillouin zone from the\n * reciprocal lattice vectors, mirroring `seekpath.brillouinzone.BZ`.\n \n The output matches the `faces_data` consumed by the\n * `brillouinzone-visualizer` web widget:\n * - `triangles_vertices`: all polyhedron vertices\n * - `triangles`: index triples (fan-triangulated convex faces)\n * - `faces`: the flat faces as lists of vertex coordinates\n /\n\nimport { Vector } from \"@/core/matrix/vector\";\nimport { dot, cross, norm } from \"@/core/matrix/operations/vector\";\n\n/* Round a vector direction to a stable key so ±parallel G-vectors collide. /\nfunction directionKey(v: Vector): string {\n const n = norm(v);\n const x = Math.round((v[0] / n) 1e6);\n const y = Math.round((v[1] / n) * 1e6);\n const z = Math.round((v[2] / n) * 1e6);\n return `${x},${y},${z}`;\n}\n\nfunction vertexKey(v: Vector, eps = 1e-6): string {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\n/*\n Solve the 3x3 system A x = d via Cramer's rule. Returns null if singular.\n * Kept local: the lib `solve` throws on singular matrices, but the corner\n * search needs a null result for near-degenerate plane intersections.\n /\nfunction solve3(A: Vector[], d: number[], tolerance: number): Vector \| null {\n const det = A[0][0] (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n if (Math.abs(det) < tolerance) return null;\n\n const detX = d[0] * (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (d[1] * A[2][2] - A[1][2] * d[2]) +\n A[0][2] * (d[1] * A[2][1] - A[1][1] * d[2]);\n const detY = A[0][0] * (d[1] * A[2][2] - A[1][2] * d[2]) -\n d[0] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * d[2] - d[1] * A[2][0]);\n const detZ = A[0][0] * (A[1][1] * d[2] - d[1] * A[2][1]) -\n A[0][1] * (A[1][0] * d[2] - d[1] * A[2][0]) +\n d[0] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n return new Float64Array([detX / det, detY / det, detZ / det]);\n}\n\nexport interface BZPolyhedron {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n}\n\n/*\n Compute the first Brillouin zone polyhedron from the reciprocal lattice\n * vectors b1, b2, b3 (rows of the reciprocal lattice matrix).\n /\nexport function getBZPolyhedron(\n b1: number[],\n b2: number[],\n b3: number[],\n supercellSize = 3,\n): BZPolyhedron {\n const r1 = new Float64Array(b1);\n const r2 = new Float64Array(b2);\n const r3 = new Float64Array(b3);\n\n // Reciprocal lattice points, keeping the shortest G-vector per direction\n const best: Map<string, { g: Vector; length2: number }> = new Map();\n for (let i = -supercellSize; i <= supercellSize; i++) {\n for (let j = -supercellSize; j <= supercellSize; j++) {\n for (let k = -supercellSize; k <= supercellSize; k++) {\n if (i === 0 && j === 0 && k === 0) continue;\n const g = new Float64Array([\n i r1[0] + j * r2[0] + k * r3[0],\n i * r1[1] + j * r2[1] + k * r3[1],\n i * r1[2] + j * r2[2] + k * r3[2],\n ]);\n const key = directionKey(g);\n const length2 = dot(g, g);\n const existing = best.get(key);\n if (!existing \|\| length2 < existing.length2) {\n best.set(key, { g, length2 });\n }\n }\n }\n }\n\n // Planes: perpendicular bisectors of the G-vectors (normals g, offset \|g\|^2/2).\n // The faces of the BZ are always among the nearest reciprocal lattice\n // directions, so restricting to the shortest ones is safe and fast.\n const MAX_PLANES = 40;\n const planes: { g: Vector; offset: number }[] = [...best.values()]\n .sort((a, b) => a.length2 - b.length2)\n .slice(0, MAX_PLANES)\n .map(({ g }) => ({ g, offset: dot(g, g) / 2 }));\n\n // Candidate BZ corners: intersections of three planes inside all planes\n const tolerance = 1e-10;\n const corners: Vector[] = [];\n const n = planes.length;\n for (let i = 0; i < n; i++) {\n for (let j = i + 1; j < n; j++) {\n for (let k = j + 1; k < n; k++) {\n const v = solve3(\n [planes[i].g, planes[j].g, planes[k].g],\n [planes[i].offset, planes[j].offset, planes[k].offset],\n tolerance,\n );\n if (!v) continue;\n let inside = true;\n for (const p of planes) {\n if (dot(p.g, v) > p.offset + tolerance) {\n inside = false;\n break;\n }\n }\n if (inside) corners.push(v);\n }\n }\n }\n\n // Deduplicate the corners\n const cornerMap: Map<string, Vector> = new Map();\n for (const v of corners) {\n const key = vertexKey(v);\n if (!cornerMap.has(key)) cornerMap.set(key, v);\n }\n const vertices = [...cornerMap.values()];\n\n // Group the corners that lie on each face plane; the face of the BZ is a\n // convex polygon of these coplanar vertices\n const faces: Vector[][] = [];\n const triangles: number[][] = [];\n const trianglesVertices: Vector[] = [];\n const vertexIndex: Map<string, number> = new Map();\n\n const addVertex = (v: Vector): number => {\n const key = vertexKey(v);\n let idx = vertexIndex.get(key);\n if (idx === undefined) {\n idx = trianglesVertices.length;\n vertexIndex.set(key, idx);\n trianglesVertices.push(v);\n }\n return idx;\n };\n\n for (const p of planes) {\n const on = vertices.filter(\n (v) => Math.abs(dot(p.g, v) - p.offset) < 1e-6,\n );\n if (on.length < 3) continue;\n\n // Sort the coplanar vertices angularly around the face centroid\n const centroid = [\n on.reduce((s, v) => s + v[0], 0) / on.length,\n on.reduce((s, v) => s + v[1], 0) / on.length,\n on.reduce((s, v) => s + v[2], 0) / on.length,\n ];\n const gx = Math.abs(p.g[0]);\n const gy = Math.abs(p.g[1]);\n const gz = Math.abs(p.g[2]);\n const ref =\n gx <= gy && gx <= gz\n ? new Float64Array([1, 0, 0])\n : gy <= gz\n ? new Float64Array([0, 1, 0])\n : new Float64Array([0, 0, 1]);\n let e1 = cross(p.g, ref);\n const e1Norm = norm(e1);\n e1 = new Float64Array([e1[0] / e1Norm, e1[1] / e1Norm, e1[2] / e1Norm]);\n const e2 = cross(p.g, e1);\n\n const ordered = [...on].sort((a, b) => {\n const da = new Float64Array([\n a[0] - centroid[0],\n a[1] - centroid[1],\n a[2] - centroid[2],\n ]);\n const db = new Float64Array([\n b[0] - centroid[0],\n b[1] - centroid[1],\n b[2] - centroid[2],\n ]);\n const angleA = Math.atan2(dot(da, e2), dot(da, e1));\n const angleB = Math.atan2(dot(db, e2), dot(db, e1));\n return angleA - angleB;\n });\n\n faces.push(ordered);\n\n // Fan triangulation of the face\n const first = addVertex(ordered[0]);\n for (let m = 1; m < ordered.length - 1; m++) {\n triangles.push([first, addVertex(ordered[m]), addVertex(ordered[m + 1])]);\n }\n }\n\n return {\n triangles_vertices: trianglesVertices.map((v) => Array.from(v)),\n triangles,\n faces: faces.map((face) => face.map((v) => Array.from(v))),\n };\n}\n","// prettier-ignore\n/** Space group data array indexed by space group number: [bravais_letter, centering, chiral]. /\nexport const spgroup_data: ([string, string, boolean] \| null)[] = [\n null, // unused (SG = 0)\n [\"a\",\"P\", false], [\"a\",\"P\", true], [\"m\",\"P\", false], [\"m\",\"P\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", false], [\"m\",\"P\", false], [\"m\",\"C\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], \n [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], \n [\"o\",\"C\", false], [\"o\",\"F\", false], [\"o\",\"I\", false], [\"o\",\"I\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false],\n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], [\"o\",\"C\", false],\n [\"o\",\"C\", false], [\"o\",\"A\", false], [\"o\",\"A\", false], [\"o\",\"A\", false],\n [\"o\",\"A\", false], [\"o\",\"F\", false], [\"o\",\"F\", false], [\"o\",\"I\", false],\n [\"o\",\"I\", false], [\"o\",\"I\", false], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"F\", true], [\"o\",\"F\", true], [\"o\",\"I\", true], [\"o\",\"I\", true],\n [\"o\",\"I\", true], [\"o\",\"I\", true], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true],\n [\"t\",\"I\", true], [\"t\",\"I\", true], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"R\", true],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], \n [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", true], [\"h\",\"R\", true], [\"h\",\"R\", true], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true],\n [\"h\",\"P\", true], [\"h\",\"P\", true], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", true],\n [\"c\",\"P\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"I\", true], \n [\"c\",\"P\", true], [\"c\",\"I\", true], [\"c\",\"P\", false], [\"c\",\"P\", false], \n [\"c\",\"F\", false], [\"c\",\"F\", false], [\"c\",\"I\", false], [\"c\",\"P\", false],\n [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false], [\"c\",\"I\", false],\n [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true],\n [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], \n [\"c\",\"I\", true], [\"c\",\"I\", true]];\n\n// prettier-ignore\n/* Centering symbols for each space group (1-indexed). /\nexport const centering: string[] = [\n \"P\",\"P\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"P\",\n \"P\",\"C\",\"C\",\"F\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\n \"C\",\"A\",\"A\",\"A\",\"A\",\"F\",\"F\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\"C\",\"C\",\"C\",\"C\",\"F\",\"F\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"R\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\n \"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"F\",\"I\",\"P\",\n \"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"P\",\"I\",\"P\",\"F\",\n \"I\",\"P\",\"F\",\"I\",\"P\",\"P\",\"P\",\"P\",\"F\",\"F\",\"F\",\"F\",\"I\",\"I\"];\n","/\n Niggli reduction of a lattice basis.\n \n Produces the unique, canonical (Niggli) cell of a 3D lattice. The lattice is\n * given as a 3×3 matrix whose rows are the lattice vectors. The result is a\n * reduced basis spanning the same lattice, together with the unimodular\n * transformation matrix `T` such that `reduced = T × original` (row vectors).\n \n Unlike LLL (which returns a short basis), Niggli reduction is a\n * normalization: its result is unique, which is why seekpath and\n * crystallography use it (e.g. to canonicalise the triclinic aP cell).\n \n This is a faithful port of spglib's `niggli_reduce` (Grosse-Kunstleve\n * 8-step algorithm), using the same `eps` tolerance semantics. The exported\n * `niggli` operates on row-vector bases and produces output matching spglib's\n * `niggli_reduce` for the same row-major lattice array.\n \n The iteration is hand-unrolled: no step-transform matrices are materialised\n * and no generic 3×3 matrix multiplication runs in the hot path. Each step is\n * a sparse in-place row operation on the basis (a permutation/sign-flip or a\n * single-row shear), which is far cheaper than a general matmul.\n \n The basis is kept in the same row-vector arrangement as the public API, so\n * no transposition is ever needed: the input is reduced in place and returned\n * directly. The Gram matrix is symmetric, so the metric and its analytic\n * updates are identical whether the vectors are treated as rows or columns;\n * only the orientation of the sparse in-place mutations differs.\n \n @see https://github.com/spglib/spglib/blob/master/src/niggli.c\n /\n\nimport { Matrix } from \"../../matrix\";\n\ninterface KernelOut {\n l: number;\n m: number;\n n: number;\n ok: boolean;\n}\n\nfunction niggliKernel(\n input: Float64Array,\n basis: Float64Array,\n transform: Float64Array \| null,\n eps: number,\n out: KernelOut,\n): void {\n const r = transform;\n\n // Scalarized 3×3 basis (rows are lattice vectors). Operated on directly and\n // written back to `basis` only once the reduction converges.\n let b00 = input[0];\n let b01 = input[1];\n let b02 = input[2];\n let b10 = input[3];\n let b11 = input[4];\n let b12 = input[5];\n let b20 = input[6];\n let b21 = input[7];\n let b22 = input[8];\n\n // Scalarized accumulated unimodular transform T (starts as identity). The\n // same sparse row ops applied to the basis are applied here, so at the end\n // reduced = T × original. Written back to `transform` only at the end.\n let x00 = r ? r[0] : 1;\n let x01 = r ? r[1] : 0;\n let x02 = r ? r[2] : 0;\n let x10 = r ? r[3] : 0;\n let x11 = r ? r[4] : 1;\n let x12 = r ? r[5] : 0;\n let x20 = r ? r[6] : 0;\n let x21 = r ? r[7] : 0;\n let x22 = r ? r[8] : 1;\n\n // --- Initial metric parameters ---\n let A = b00 b00 + b01 * b01 + b02 * b02;\n let B = b10 * b10 + b11 * b11 + b12 * b12;\n let C = b20 * b20 + b21 * b21 + b22 * b22;\n let zeta = 2 * (b00 * b10 + b01 * b11 + b02 * b12);\n let eta = 2 * (b00 * b20 + b01 * b21 + b02 * b22);\n let xi = 2 * (b10 * b20 + b11 * b21 + b12 * b22);\n\n let l = 0;\n let m = 0;\n let n = 0;\n\n const maxAttempts = 1000;\n for (let attempt = 0; attempt < maxAttempts; attempt++) {\n // ---- Step 1: r0 = −r1, r1 = −r0, r2 = −r2 ----\n // (A,B,C,xi,eta,zeta) -> (B,A,C,eta,xi,zeta)\n if (A > B + eps \|\| (Math.abs(A - B) <= eps && Math.abs(xi) > Math.abs(eta) + eps)) {\n let t00 = b00;\n b00 = -b10; b10 = -t00;\n let t01 = b01;\n b01 = -b11; b11 = -t01;\n let t02 = b02;\n b02 = -b12; b12 = -t02;\n b20 = -b20; b21 = -b21; b22 = -b22;\n let xt00 = x00;\n x00 = -x10; x10 = -xt00;\n let xt01 = x01;\n x01 = -x11; x11 = -xt01;\n let xt02 = x02;\n x02 = -x12; x12 = -xt02;\n x20 = -x20; x21 = -x21; x22 = -x22;\n const tA = A;\n const txi = xi;\n A = B;\n B = tA;\n xi = eta;\n eta = txi;\n }\n\n // ---- Step 2: r0 = −r0, r1 = −r2, r2 = −r1 ----\n // (A,B,C,xi,eta,zeta) -> (A,C,B,xi,zeta,eta)\n if (B > C + eps \|\| (Math.abs(B - C) <= eps && Math.abs(eta) > Math.abs(zeta) + eps)) {\n b00 = -b00; b01 = -b01; b02 = -b02;\n let t0 = b10;\n b10 = -b20; b20 = -t0;\n let t1 = b11;\n b11 = -b21; b21 = -t1;\n let t2 = b12;\n b12 = -b22; b22 = -t2;\n x00 = -x00; x01 = -x01; x02 = -x02;\n let xt0 = x10;\n x10 = -x20; x20 = -xt0;\n let xt1 = x11;\n x11 = -x21; x21 = -xt1;\n let xt2 = x12;\n x12 = -x22; x22 = -xt2;\n const tB = B;\n const teta = eta;\n B = C;\n C = tB;\n eta = zeta;\n zeta = teta;\n continue;\n }\n\n // ---- Step 3: sign flip so l·m·n = 1 ----\n l = xi < -eps ? -1 : xi > eps ? 1 : 0;\n m = eta < -eps ? -1 : eta > eps ? 1 : 0;\n n = zeta < -eps ? -1 : zeta > eps ? 1 : 0;\n const lmn = l * m * n;\n if (lmn === 1) {\n const i = l === -1 ? -1 : 1;\n const j = m === -1 ? -1 : 1;\n const k = n === -1 ? -1 : 1;\n b00 = i; b01 = i; b02 = i;\n b10 = j; b11 = j; b12 = j;\n b20 = k; b21 = k; b22 = k;\n x00 = i; x01 = i; x02 = i;\n x10 = j; x11 = j; x12 = j;\n x20 = k; x21 = k; x22 = k;\n zeta = i j;\n eta = i k;\n xi = j k;\n }\n\n // ---- Step 4: further sign flips when l·m·n ∈ {0, −1} ----\n if (!(l === -1 && m === -1 && n === -1)) {\n if (lmn === 0 \|\| lmn === -1) {\n let i = 1;\n let j = 1;\n let k = 1;\n let which = -1;\n if (l === 1) i = -1;\n if (l === 0) which = 0;\n if (m === 1) j = -1;\n if (m === 0) which = 1;\n if (n === 1) k = -1;\n if (n === 0) which = 2;\n\n if (i * j * k === -1) {\n if (which === 0) i = -1;\n if (which === 1) j = -1;\n if (which === 2) k = -1;\n }\n\n b00 = i; b01 = i; b02 = i;\n b10 = j; b11 = j; b12 = j;\n b20 = k; b21 = k; b22 = k;\n x00 = i; x01 = i; x02 = i;\n x10 = j; x11 = j; x12 = j;\n x20 = k; x21 = k; x22 = k;\n zeta = i j;\n eta = i k;\n xi = j k;\n }\n }\n\n // ---- Step 5: r2 += sign · r1 ----\n if (\n Math.abs(xi) > B + eps \|\|\n (Math.abs(B - xi) <= eps && 2 * eta < zeta - eps) \|\|\n (Math.abs(B + xi) <= eps && zeta < -eps)\n ) {\n const s: number = xi > 0 ? -1 : 1;\n b20 += s * b10; b21 += s * b11; b22 += s * b12;\n x20 += s * x10; x21 += s * x11; x22 += s * x12;\n C += s * xi + B;\n xi = xi + 2 * s * B;\n eta = eta + s * zeta;\n continue;\n }\n\n // ---- Step 6: r2 += sign · r0 ----\n if (\n Math.abs(eta) > A + eps \|\|\n (Math.abs(A - eta) <= eps && 2 * xi < zeta - eps) \|\|\n (Math.abs(A + eta) <= eps && zeta < -eps)\n ) {\n const s: number = eta > 0 ? -1 : 1;\n b20 += s * b00; b21 += s * b01; b22 += s * b02;\n x20 += s * x00; x21 += s * x01; x22 += s * x02;\n C += s * eta + A;\n xi = xi + s * zeta;\n eta = eta + 2 * s * A;\n continue;\n }\n\n // ---- Step 7: r1 += sign · r0 ----\n if (\n Math.abs(zeta) > A + eps \|\|\n (Math.abs(A - zeta) <= eps && 2 * xi < eta - eps) \|\|\n (Math.abs(A + zeta) <= eps && eta < -eps)\n ) {\n const s: number = zeta > 0 ? -1 : 1;\n b10 += s * b00; b11 += s * b01; b12 += s * b02;\n x10 += s * x00; x11 += s * x01; x12 += s * x02;\n B += s * zeta + A;\n xi = xi + s * eta;\n zeta = zeta + 2 * s * A;\n continue;\n }\n\n // ---- Step 8: r2 += r0 + r1 ----\n {\n const sum = xi + eta + zeta + A + B;\n if (\n sum < -eps \|\|\n (Math.abs(sum) <= eps && 2 * (A + eta) + zeta > eps)\n ) {\n b20 += b00 + b10; b21 += b01 + b11; b22 += b02 + b12;\n x20 += x00 + x10; x21 += x01 + x11; x22 += x02 + x12;\n C += A + B + xi + eta + zeta;\n xi = xi + zeta + 2 * B;\n eta = eta + zeta + 2 * A;\n continue;\n }\n }\n\n // No step fired: converged.\n out.l = l;\n out.m = m;\n out.n = n;\n out.ok = true;\n basis[0] = b00; basis[1] = b01; basis[2] = b02;\n basis[3] = b10; basis[4] = b11; basis[5] = b12;\n basis[6] = b20; basis[7] = b21; basis[8] = b22;\n if (r) {\n r[0] = x00; r[1] = x01; r[2] = x02;\n r[3] = x10; r[4] = x11; r[5] = x12;\n r[6] = x20; r[7] = x21; r[8] = x22;\n }\n return;\n }\n\n basis[0] = b00; basis[1] = b01; basis[2] = b02;\n basis[3] = b10; basis[4] = b11; basis[5] = b12;\n basis[6] = b20; basis[7] = b21; basis[8] = b22;\n if (r) {\n r[0] = x00; r[1] = x01; r[2] = x02;\n r[3] = x10; r[4] = x11; r[5] = x12;\n r[6] = x20; r[7] = x21; r[8] = x22;\n }\n out.ok = false;\n}\n\nexport interface NiggliResult {\n /** The Niggli-reduced basis (3×3, rows are lattice vectors). /\n basis: Matrix;\n /\n The unimodular transformation matrix `T` such that\n * `reduced = T × original` (row-vector convention).\n /\n transform: Matrix;\n}\n\n/\n Reduce a 3×3 lattice basis (rows = lattice vectors) to its unique Niggli\n * cell.\n \n @param input A 3×3 matrix whose rows are the lattice vectors.\n * @param eps Tolerance against which near-equalities are decided. Mirrors\n * spglib's `symprec` (default `1e-5`).\n * @returns The reduced basis and transformation, or `null` if reduction did\n * not converge.\n /\nexport function niggli(input: Matrix, eps = 1e-5): NiggliResult \| null {\n if (input.rows !== 3 \|\| input.cols !== 3) {\n throw new Error(\n `niggli requires a 3x3 matrix, got ${input.rows}×${input.cols}`,\n );\n }\n\n // The basis is kept in row-vector form throughout (rows are the lattice\n // vectors), so the input is reduced directly and the result returned as-is;\n // no transposition is needed. `rightTransform` accumulates the same row\n // operations, yielding directly the left-multiply form `reduced = T × input`.\n const basis = new Float64Array(input.data);\n const transform = new Float64Array([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n const out: KernelOut = { l: 0, m: 0, n: 0, ok: false };\n niggliKernel(input.data, basis, transform, eps, out);\n if (!out.ok) return null;\n\n // `basis` is a private working copy (never the caller's input) and\n // `transform` is integer-valued, so wrap them directly as the result\n // matrices without an extra array copy.\n return {\n basis: { rows: 3, cols: 3, data: basis },\n transform: { rows: 3, cols: 3, data: transform },\n };\n}\n","import { Matrix, createMatrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { scale } from \"@/core/matrix/operations/scale\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\n\nconst TWO_PI = 2 Math.PI;\n\n/** Build a 3x3 Matrix from 9 row-major values. /\nexport function matrixFromRowMajor(data: ArrayLike<number>): Matrix {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return createMatrix(3, 3, Array.from(data));\n}\n\n/\n Return [a, b, c, cosalpha, cosbeta, cosgamma] for a 3x3 lattice whose\n * rows are the lattice vectors.\n /\nexport function cellParams(\n lattice: Matrix,\n): [number, number, number, number, number, number] {\n const d = lattice.data;\n const v1 = [d[0], d[1], d[2]];\n const v2 = [d[3], d[4], d[5]];\n const v3 = [d[6], d[7], d[8]];\n const a = Math.hypot(v1[0], v1[1], v1[2]);\n const b = Math.hypot(v2[0], v2[1], v2[2]);\n const c = Math.hypot(v3[0], v3[1], v3[2]);\n const dot = (u: number[], v: number[]) =>\n u[0] v[0] + u[1] * v[1] + u[2] * v[2];\n const cosalpha = dot(v2, v3) / b / c;\n const cosbeta = dot(v1, v3) / a / c;\n const cosgamma = dot(v1, v2) / a / b;\n return [a, b, c, cosalpha, cosbeta, cosgamma];\n}\n\n/** Reciprocal-space cell rows, such that dot(real, recip.T) = 2π I. /\nexport function getReciprocalCellRows(real: Matrix): Matrix {\n return transpose(scale(gjInverse(real), TWO_PI));\n}\n\n/* Real-space cell rows given reciprocal rows, such that dot(recip, real.T) = 2π I. /\nexport function getRealCellFromReciprocalRows(recip: Matrix): Matrix {\n return transpose(scale(gjInverse(recip), TWO_PI));\n}\n\n/\n Return the (P, invP) transformation matrices from the crystallographic\n * conventional cell to the primitive cell, as in Table 3 of the HPKOT paper:\n * (a_P, b_P, c_P) = (a, b, c) P and (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T.\n /\nexport function getPmatrix(\n bravaisLattice: string,\n): { P: number[][]; invP: number[][] } {\n if ([\"cP\", \"tP\", \"hP\", \"oP\", \"mP\"].includes(bravaisLattice)) {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if ([\"cF\", \"oF\"].includes(bravaisLattice)) {\n return {\n P: [\n [0, 0.5, 0.5],\n [0.5, 0, 0.5],\n [0.5, 0.5, 0],\n ],\n invP: [\n [-1, 1, 1],\n [1, -1, 1],\n [1, 1, -1],\n ],\n };\n }\n if ([\"cI\", \"tI\", \"oI\"].includes(bravaisLattice)) {\n return {\n P: [\n [-0.5, 0.5, 0.5],\n [0.5, -0.5, 0.5],\n [0.5, 0.5, -0.5],\n ],\n invP: [\n [0, 1, 1],\n [1, 0, 1],\n [1, 1, 0],\n ],\n };\n }\n if (bravaisLattice === \"hR\") {\n return {\n P: [\n [2 / 3, -1 / 3, -1 / 3],\n [1 / 3, 1 / 3, -2 / 3],\n [1 / 3, 1 / 3, 1 / 3],\n ],\n invP: [\n [1, 0, 1],\n [-1, 1, 1],\n [0, -1, 1],\n ],\n };\n }\n if (bravaisLattice === \"oC\") {\n return {\n P: [\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, -1, 0],\n [1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"oA\") {\n return {\n P: [\n [0, 0, 1],\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n ],\n invP: [\n [0, 1, -1],\n [0, 1, 1],\n [1, 0, 0],\n ],\n };\n }\n if (bravaisLattice === \"mC\") {\n return {\n P: [\n [0.5, -0.5, 0],\n [0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 1, 0],\n [-1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"aP\") {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n throw new Error(`Invalid bravais_lattice ${bravaisLattice}`);\n}\n\nexport interface PrimitiveCellResult {\n lattice: number[][];\n positions: number[][];\n types: number[];\n mapping: number[];\n}\n\n/\n Build the crystallographic primitive cell from a standardized conventional\n * cell using the HPKOT P matrices, deduplicating atoms that coincide modulo 1.\n /\nexport function getPrimitive(\n lattice: number[][],\n positions: number[][],\n types: number[],\n bravaisLattice: string,\n threshold = 1e-6,\n): PrimitiveCellResult {\n const { P, invP } = getPmatrix(bravaisLattice);\n\n const volumeRatio = Math.round(Math.abs(det3(invP)));\n\n // (a_P, b_P, c_P) = (a, b, c) P => prim vector j = sum_k P[k][j] a_k,\n // i.e. prim_lattice = P^T @ lattice\n const primLattice = matmul3(transpose3(P), lattice);\n // (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T => row-vector form: positions @ invP.T\n const primPositions = matmul3(positions, transpose3(invP));\n\n const n = positions.length;\n\n // Mark equivalent atoms (same position modulo 1, shifted so that ±0.5 wrap)\n const match = (u: number, v: number) => {\n const diff = Math.abs(((u - v + 0.5) % 1 + 1) % 1 - 0.5);\n return diff < threshold;\n };\n\n const groups: number[][] = [];\n const assigned = new Array<boolean>(n).fill(false);\n\n for (let i = 0; i < n; i++) {\n if (assigned[i]) continue;\n const group: number[] = [];\n for (let j = i; j < n; j++) {\n if (\n match(primPositions[j][0], primPositions[i][0]) &&\n match(primPositions[j][1], primPositions[i][1]) &&\n match(primPositions[j][2], primPositions[i][2])\n ) {\n group.push(j);\n assigned[j] = true;\n }\n }\n groups.push(group);\n }\n\n for (const group of groups) {\n if (group.length !== volumeRatio) {\n throw new Error(\n `Problem creating primitive cell, found group of atoms with length ${group.length} != ${volumeRatio}`,\n );\n }\n const typeSet = new Set(group.map((idx) => types[idx]));\n if (typeSet.size !== 1) {\n throw new Error(\n \"The following atoms go on top of each other, but they are of different type!\",\n );\n }\n }\n\n groups.sort((a, b) => a[0] - b[0]);\n\n const mapping = new Array<number>(n).fill(-1);\n for (let primIdx = 0; primIdx < groups.length; primIdx++) {\n for (const atIdx of groups[primIdx]) mapping[atIdx] = primIdx;\n }\n\n return {\n lattice: primLattice,\n positions: groups.map((g) => primPositions[g[0]]),\n types: groups.map((g) => types[g[0]]),\n mapping,\n };\n}\n\nfunction transpose3(m: number[][]): number[][] {\n return [\n [m[0][0], m[1][0], m[2][0]],\n [m[0][1], m[1][1], m[2][1]],\n [m[0][2], m[1][2], m[2][2]],\n ];\n}\n\nfunction matmul3(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] * b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nfunction det3(m: number[][]): number {\n return (\n m[0][0] * (m[1][1] * m[2][2] - m[1][2] * m[2][1]) -\n m[0][1] * (m[1][0] * m[2][2] - m[1][2] * m[2][0]) +\n m[0][2] * (m[1][0] * m[2][1] - m[1][1] * m[2][0])\n );\n}\n\n/** Evaluate an expression that only requires precomputed k-parameters. /\nexport function evalExprSimple(expr: string, kparam: Record<string, number>): number {\n switch (expr) {\n case \"0\":\n return 0;\n case \"1/2\":\n return 0.5;\n case \"1\":\n return 1;\n case \"-1/2\":\n return -0.5;\n case \"1/4\":\n return 0.25;\n case \"3/8\":\n return 0.375;\n case \"3/4\":\n return 0.75;\n case \"5/8\":\n return 0.625;\n case \"1/3\":\n return 1 / 3;\n default: {\n const val = kparam[expr];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${expr}' in eval_expr_simple but this has not been defined or not yet computed`,\n );\n }\n return val;\n }\n }\n}\n\n/* Extend kparam with derived expressions (1-x, -x, 1/2-x, ...). /\nexport function extendKparam(kparam: Record<string, number>): Record<string, number> {\n const extended: Record<string, number> = {};\n for (const [key, val] of Object.entries(kparam)) {\n extended[key] = val;\n extended[`-${key}`] = -val;\n extended[`1-${key}`] = 1 - val;\n extended[`-1+${key}`] = -1 + val;\n extended[`1/2-${key}`] = 0.5 - val;\n extended[`1/2+${key}`] = 0.5 + val;\n }\n return extended;\n}\n\n/\n Evaluate a k-parameter expression as a function of the cell parameters and\n * previously computed k-parameters. Mirrors the hardcoded table in seekpath.\n /\nexport function evalExpr(\n expr: string,\n a: number,\n b: number,\n c: number,\n cosalpha: number,\n cosbeta: number,\n cosgamma: number,\n kparam: Record<string, number>,\n): number {\n const sinbeta = Math.sqrt(1 - cosbeta cosbeta);\n\n const k = (name: string): number => {\n const val = kparam[name];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${name}' but this has not been defined or not yet computed`,\n );\n }\n return val;\n };\n const Z = () => k(\"Z\");\n const E = () => k(\"E\");\n const F = () => k(\"F\");\n const U = () => k(\"U\");\n const W = () => k(\"W\");\n const S = () => k(\"S\");\n const M = () => k(\"M\");\n const X = () => k(\"X\");\n const D = () => k(\"D\");\n const Y = () => k(\"Y\");\n\n switch (expr) {\n case \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\":\n return (a * a / b / b + (1 + a / c * cosbeta) / sinbeta / sinbeta) / 4;\n case \"1-Zbb/a/a\":\n return 1 - Z() * b * b / a / a;\n case \"1/2-2Zccosbeta/a\":\n return 0.5 - 2 Z() * c * cosbeta / a;\n case \"E/2+aa/4/b/b+accosbeta/2/b/b\":\n return E() / 2 + a a / 4 / b / b + a * c * cosbeta / 2 / b / b;\n case \"2F-Z\":\n return 2 F() - Z();\n case \"c/2/a/cosbeta(1-4U+aasinbetasinbeta/b/b)\":\n return (\n c / 2 / a / cosbeta (1 - 4 * U() + a * a * sinbeta * sinbeta / b / b)\n );\n case \"-1/4+W/2-Zccosbeta/a\":\n return -0.25 + W() / 2 - Z() * c * cosbeta / a;\n case \"(2+a/ccosbeta)/4/sinbeta/sinbeta\":\n return (2 + a / c cosbeta) / 4 / sinbeta / sinbeta;\n case \"3/4-bb/4/a/a/sinbeta/sinbeta\":\n return 3 / 4 - b b / 4 / a / a / sinbeta / sinbeta;\n case \"S-(3/4-S)acosbeta/c\":\n return S() - (3 / 4 - S()) * a * cosbeta / c;\n case \"(1+aa/b/b)/4\":\n return (1 + a a / b / b) / 4;\n case \"-accosbeta/2/b/b\":\n return -a * c * cosbeta / 2 / b / b;\n case \"1+Z-2M\":\n return 1 + Z() - 2 M();\n case \"X-2D\":\n return X() - 2 D();\n case \"(1+a/ccosbeta)/2/sinbeta/sinbeta\":\n return (1 + a / c cosbeta) / 2 / sinbeta / sinbeta;\n case \"1/2+Yccosbeta/a\":\n return 0.5 + Y() * c * cosbeta / a;\n case \"aa/4/c/c\":\n return a a / 4 / c / c;\n case \"5/6-2D\":\n return 5 / 6 - 2 D();\n case \"1/3+D\":\n return 1 / 3 + D();\n case \"1/6-cc/9/a/a\":\n return 1 / 6 - c c / 9 / a / a;\n case \"1/2-2Z\":\n return 0.5 - 2 Z();\n case \"1/2+Z\":\n return 0.5 + Z();\n case \"(1+bb/c/c)/4\":\n return (1 + b b / c / c) / 4;\n case \"(1+cc/b/b)/4\":\n return (1 + c c / b / b) / 4;\n case \"(1+bb/a/a)/4\":\n return (1 + b b / a / a) / 4;\n case \"(1+aa/b/b-aa/c/c)/4\":\n return (1 + a * a / b / b - a * a / c / c) / 4;\n case \"(1+aa/b/b+aa/c/c)/4\":\n return (1 + a * a / b / b + a * a / c / c) / 4;\n case \"(1+cc/a/a-cc/b/b)/4\":\n return (1 + c * c / a / a - c * c / b / b) / 4;\n case \"(1+cc/a/a+cc/b/b)/4\":\n return (1 + c * c / a / a + c * c / b / b) / 4;\n case \"(1+bb/a/a-bb/c/c)/4\":\n return (1 + b * b / a / a - b * b / c / c) / 4;\n case \"(1+cc/b/b-cc/a/a)/4\":\n return (1 + c * c / b / b - c * c / a / a) / 4;\n case \"(1+aa/c/c)/4\":\n return (1 + a a / c / c) / 4;\n case \"(bb-aa)/4/c/c\":\n return (b * b - a * a) / 4 / c / c;\n case \"(aa+bb)/4/c/c\":\n return (a * a + b * b) / 4 / c / c;\n case \"(1+cc/a/a)/4\":\n return (1 + c c / a / a) / 4;\n case \"(cc-bb)/4/a/a\":\n return (c * c - b * b) / 4 / a / a;\n case \"(bb+cc)/4/a/a\":\n return (b * b + c * c) / 4 / a / a;\n case \"(aa-cc)/4/b/b\":\n return (a * a - c * c) / 4 / b / b;\n case \"(cc+aa)/4/b/b\":\n return (c * c + a * a) / 4 / b / b;\n case \"aa/2/c/c\":\n return a a / 2 / c / c;\n default:\n throw new Error(\n `Unknown expression, define a new case: '${expr}'`,\n );\n }\n}\n\n/** Wrap a cell in a Matrix to use matrix helpers. /\nexport function toMatrix(rows: number[][]): Matrix {\n return createMatrix(3, 3, rows.flat());\n}\n\n/* Row-vector times matrix: x_abs[i] = v . col_i(m). /\nexport function vecMulMat(v: readonly number[], m: number[][]): number[] {\n return [\n v[0] m[0][0] + v[1] * m[1][0] + v[2] * m[2][0],\n v[0] * m[0][1] + v[1] * m[1][1] + v[2] * m[2][1],\n v[0] * m[0][2] + v[1] * m[1][2] + v[2] * m[2][2],\n ];\n}\n","import { Matrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\nimport { niggli } from \"@/core/matrix/operations/reduction/niggli\";\nimport {\n cellParams,\n getReciprocalCellRows,\n getRealCellFromReciprocalRows,\n matrixFromRowMajor,\n} from \"./seekpathTools\";\n\nconst M2_MATRICES = [\n [\n [0, 0, 1],\n [1, 0, 0],\n [0, 1, 0],\n ],\n [\n [0, 1, 0],\n [0, 0, 1],\n [1, 0, 0],\n ],\n [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n];\n\n/** Determine the aP label (aP2 all-obtuse / aP3 all-acute) as in HPKOT. /\nconst M3_I = [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n];\nconst M3_XX = [\n [1, 0, 0],\n [0, -1, 0],\n [0, 0, -1],\n];\nconst M3_YY = [\n [-1, 0, 0],\n [0, 1, 0],\n [0, 0, -1],\n];\nconst M3_ZZ = [\n [-1, 0, 0],\n [0, -1, 0],\n [0, 0, 1],\n];\n\nfunction mulRows(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nexport interface APTransform {\n lattice: number[][];\n positions: number[][];\n extBravais: string;\n}\n\n/*\n Apply the Niggli reduction plus the M2/M3 vector transforms of the HPKOT\n * paper to bring a triclinic conventional cell into the all-obtuse (aP2) or\n * all-acute (aP3) setting.\n /\nexport async function transformAP(\n lattice: number[][],\n positions: number[][],\n): Promise<APTransform> {\n const convLattice = matrixFromRowMajor(lattice.flat());\n\n const reciprocalCellOrig = getReciprocalCellRows(convLattice);\n const reduced = niggli(reciprocalCellOrig);\n if (!reduced) throw new Error(\"Niggli reduction failed for aP lattice\");\n const reciprocalCell2 = reduced.basis;\n const realCell2 = getRealCellFromReciprocalRows(reciprocalCell2);\n\n const [ka2, kb2, kc2, coskalpha2, coskbeta2, coskgamma2] =\n cellParams(reciprocalCell2);\n const conditions = [\n Math.abs(kb2 kc2 * coskalpha2),\n Math.abs(kc2 * ka2 * coskbeta2),\n Math.abs(ka2 * kb2 * coskgamma2),\n ];\n\n let smallest = 0;\n if (conditions[1] < conditions[smallest]) smallest = 1;\n if (conditions[2] < conditions[smallest]) smallest = 2;\n const M2 = matrixFromRowMajor(M2_MATRICES[smallest].flat());\n const realCell3 = mul(transpose(M2), realCell2);\n\n const reciprocalCell3 = getReciprocalCellRows(realCell3);\n const [, , , ca3, cb3, cg3] = cellParams(reciprocalCell3);\n\n let M3: number[][];\n if ((ca3 > 0 && cb3 > 0 && cg3 > 0) \|\| (ca3 <= 0 && cb3 <= 0 && cg3 <= 0))\n M3 = M3_I;\n else if (\n (ca3 > 0 && cb3 <= 0 && cg3 <= 0) \|\|\n (ca3 <= 0 && cb3 > 0 && cg3 > 0)\n )\n M3 = M3_XX;\n else if (\n (ca3 <= 0 && cb3 > 0 && cg3 <= 0) \|\|\n (ca3 > 0 && cb3 <= 0 && cg3 > 0)\n )\n M3 = M3_YY;\n else if (\n (ca3 <= 0 && cb3 <= 0 && cg3 > 0) \|\|\n (ca3 > 0 && cb3 > 0 && cg3 <= 0)\n )\n M3 = M3_ZZ;\n else\n throw new Error(\n \"Problem identifying M3 matrix in aP lattice: sign pattern of cosines ambiguous\",\n );\n\n const M3mat = matrixFromRowMajor(M3.flat());\n const realCellFinal = mul(transpose(M3mat), realCell3);\n const reciprocalCellFinal = getReciprocalCellRows(realCellFinal);\n const [, , , ca, cb, cg] = cellParams(reciprocalCellFinal);\n\n let extBravais: string;\n if (ca <= 0 && cb <= 0 && cg <= 0) extBravais = \"aP2\";\n else if (ca >= 0 && cb >= 0 && cg >= 0) extBravais = \"aP3\";\n else\n throw new Error(\n \"Unexpected aP lattice, neither all-obtuse nor all-acute in reciprocal space\",\n );\n\n // Express the (absolute) atomic positions in the new real cell basis\n const finalRows = Array.from(realCellFinal.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const absPositions = mulRows(positions, lattice);\n const invFinal = gjInverse(matrixFromRowMajor(finalRows.flat()));\n const newPositions = absPositions.map((p) => {\n const v = createVector(p);\n const res = mul(invFinal, v).data;\n return [res[0], res[1], res[2]];\n });\n\n return {\n lattice: finalRows,\n positions: newPositions,\n extBravais,\n };\n}\n\nfunction createVector(v: number[]): Matrix {\n return { rows: 3, cols: 1, data: new Float64Array(v) };\n}\n\n/** Determine the aP label (aP2 / aP3) for a triclinic conventional lattice. /\nexport async function determineAP(convLattice: Matrix): Promise<string> {\n const rows = Array.from(convLattice.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const { extBravais } = await transformAP(rows, []);\n return extBravais;\n}\n\n/* Determine the Seekpath extended Bravais lattice from a conventional cell. /\nexport function determineExtBravais(\n bL: string,\n spgN: number,\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n): string {\n const threshold = 1e-7;\n\n switch (bL) {\n case \"cP\":\n if (spgN < 195 \|\| spgN > 230)\n throw new Error(\"cP requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cP1\" : \"cP2\";\n\n case \"cF\":\n if (spgN < 195 \|\| spgN > 230)\n throw new Error(\"cF requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cF1\" : \"cF2\";\n\n case \"cI\":\n return \"cI1\";\n\n case \"tP\":\n return \"tP1\";\n\n case \"tI\":\n if (c - a < threshold) {\n console.warn(\"tI lattice, a ≈ c\");\n }\n return c <= a ? \"tI1\" : \"tI2\";\n\n case \"oP\":\n return \"oP1\";\n\n case \"oF\": {\n const A = 1.0 / a * 2;\n const B = 1.0 / b 2;\n const C = 1.0 / c 2;\n\n if (A > B + C) {\n return \"oF1\";\n }\n\n if (C > A + B) {\n return \"oF2\";\n } else return \"oF3\";\n }\n\n case \"oI\": {\n const sorted = [\n { v: c, id: 1 },\n { v: b, id: 3 },\n { v: a, id: 2 },\n ]\n .sort((x, y) => x.v - y.v \|\| x.id - y.id)\n .reverse();\n\n if (Math.abs(sorted[0].v - sorted[1].v) < threshold) {\n console.warn(\"oI near-degeneracy\");\n }\n\n return `${bL}${sorted[0].id}`;\n }\n\n case \"oC\":\n return a <= b ? \"oC1\" : \"oC2\";\n\n case \"oA\":\n return b <= c ? \"oA1\" : \"oA2\";\n\n case \"hP\":\n return [\n 143, 144, 145, 146, 147, 148, 149, 151, 153, 157, 159, 160, 161, 162,\n 163,\n ].includes(spgN)\n ? \"hP1\"\n : \"hP2\";\n\n case \"hR\":\n return Math.sqrt(3) * a <= Math.sqrt(2) * c ? \"hR1\" : \"hR2\";\n\n case \"mP\":\n return \"mP1\";\n\n case \"mC\": {\n const rad = Math.PI / 180;\n const cosbeta = Math.cos(beta * rad);\n const sinbeta = Math.sin(beta * rad);\n\n const term1 = b - a * Math.sqrt(1 - cosbeta ** 2);\n\n if (Math.abs(term1) < threshold) {\n console.warn(\"mC near-degeneracy\");\n }\n\n if (b < a * sinbeta) return \"mC1\";\n\n const expr = (-a * cosbeta) / c + (a ** 2 * (1 - cosbeta 2)) / b 2;\n if (Math.abs(expr - 1.0) < threshold) {\n console.warn(\"mC second degeneracy\");\n }\n\n return expr <= 1 ? \"mC2\" : \"mC3\";\n }\n\n case \"aP\":\n throw new Error(\"aP must be handled by determineAP\");\n\n default:\n throw new Error(`Unknown bravais lattice: ${bL}`);\n }\n}\n","// AUTO-GENERATED FILE — DO NOT EDIT\n// Source: https://github.com/materialscloud-org/seekpath (HPKOT band path data)\n\nexport interface BandPathData {\n kparam: [string, string][];\n points: Record<string, [string, string, string]>;\n path: [string, string][];\n}\n\nexport const bandPathData: Record<string, BandPathData> = {\n \"aP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V\": [\"1/2\", \"1/2\", \"0\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"U\", \"GAMMA\"],\n [\"GAMMA\", \"V\"]\n ],\n },\n \"aP3\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"Y_2\": [\"0\", \"-1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"1/2\", \"-1/2\", \"0\"],\n \"U_2\": [\"-1/2\", \"0\", \"1/2\"],\n \"T_2\": [\"0\", \"-1/2\", \"1/2\"],\n \"R_2\": [\"-1/2\", \"-1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R_2\", \"GAMMA\"],\n [\"GAMMA\", \"T_2\"],\n [\"U_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"cF1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"],\n [\"X\", \"W_2\"]\n ],\n },\n \"cF2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"]\n ],\n },\n \"cI1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"H\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"H\"],\n [\"H\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"P\"],\n [\"P\", \"H\"],\n [\"P\", \"N\"]\n ],\n },\n \"cP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"],\n [\"M\", \"X_1\"]\n ],\n },\n \"cP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"]\n ],\n },\n \"hP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"],\n [\"K\", \"H_2\"]\n ],\n },\n \"hP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"]\n ],\n },\n \"hR1\": {\n kparam: [\n [\"D\", \"aa/4/c/c\"],\n [\"Y\", \"5/6-2D\"],\n [\"N\", \"1/3+D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"L_2\": [\"0\", \"-1/2\", \"0\"],\n \"L_4\": [\"0\", \"0\", \"-1/2\"],\n \"F\": [\"1/2\", \"0\", \"1/2\"],\n \"F_2\": [\"1/2\", \"1/2\", \"0\"],\n \"S_0\": [\"N\", \"-N\", \"0\"],\n \"S_2\": [\"1-N\", \"0\", \"N\"],\n \"S_4\": [\"N\", \"0\", \"-N\"],\n \"S_6\": [\"1-N\", \"N\", \"0\"],\n \"H_0\": [\"1/2\", \"-1+Y\", \"1-Y\"],\n \"H_2\": [\"Y\", \"1-Y\", \"1/2\"],\n \"H_4\": [\"Y\", \"1/2\", \"1-Y\"],\n \"H_6\": [\"1/2\", \"1-Y\", \"-1+Y\"],\n \"M_0\": [\"N\", \"-1+Y\", \"N\"],\n \"M_2\": [\"1-N\", \"1-Y\", \"1-N\"],\n \"M_4\": [\"Y\", \"N\", \"N\"],\n \"M_6\": [\"1-N\", \"1-N\", \"1-Y\"],\n \"M_8\": [\"N\", \"N\", \"-1+Y\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"H_2\"],\n [\"H_0\", \"L\"],\n [\"L\", \"GAMMA\"],\n [\"GAMMA\", \"S_0\"],\n [\"S_2\", \"F\"],\n [\"F\", \"GAMMA\"]\n ],\n },\n \"hR2\": {\n kparam: [\n [\"Z\", \"1/6-cc/9/a/a\"],\n [\"H\", \"1/2-2Z\"],\n [\"N\", \"1/2+Z\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P_0\": [\"H\", \"-1+H\", \"H\"],\n \"P_2\": [\"H\", \"H\", \"H\"],\n \"R_0\": [\"1-H\", \"-H\", \"-H\"],\n \"M\": [\"1-N\", \"-N\", \"1-N\"],\n \"M_2\": [\"N\", \"-1+N\", \"-1+N\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"F\": [\"1/2\", \"-1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"L\"],\n [\"L\", \"T\"],\n [\"T\", \"P_0\"],\n [\"P_2\", \"GAMMA\"],\n [\"GAMMA\", \"F\"]\n ],\n },\n \"mC1\": {\n kparam: [\n [\"Z\", \"(2+a/ccosbeta)/4/sinbeta/sinbeta\"],\n [\"H\", \"1/2-2Zccosbeta/a\"],\n [\"S\", \"3/4-bb/4/a/a/sinbeta/sinbeta\"],\n [\"P\", \"S-(3/4-S)acosbeta/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y_2\": [\"-1/2\", \"1/2\", \"0\"],\n \"Y_4\": [\"1/2\", \"-1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"C\": [\"1-S\", \"1-S\", \"0\"],\n \"C_2\": [\"-1+S\", \"S\", \"0\"],\n \"C_4\": [\"S\", \"-1+S\", \"0\"],\n \"D\": [\"-1+P\", \"P\", \"1/2\"],\n \"D_2\": [\"1-P\", \"1-P\", \"1/2\"],\n \"E\": [\"-1+Z\", \"1-Z\", \"1-H\"],\n \"E_2\": [\"-Z\", \"Z\", \"H\"],\n \"E_4\": [\"Z\", \"-Z\", \"1-H\"]\n },\n path: [\n [\"GAMMA\", \"C\"],\n [\"C_2\", \"Y_2\"],\n [\"Y_2\", \"GAMMA\"],\n [\"GAMMA\", \"M_2\"],\n [\"M_2\", \"D\"],\n [\"D_2\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC2\": {\n kparam: [\n [\"Z\", \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\"],\n [\"M\", \"(1+aa/b/b)/4\"],\n [\"D\", \"-accosbeta/2/b/b\"],\n [\"X\", \"1/2-2Zccosbeta/a\"],\n [\"P\", \"1+Z-2M\"],\n [\"S\", \"X-2D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"1/2\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"F\": [\"-1+P\", \"1-P\", \"1-S\"],\n \"F_2\": [\"1-P\", \"P\", \"S\"],\n \"F_4\": [\"P\", \"1-P\", \"1-S\"],\n \"H\": [\"-Z\", \"Z\", \"X\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-X\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-X\"],\n \"G\": [\"-M\", \"M\", \"D\"],\n \"G_2\": [\"M\", \"1-M\", \"-D\"],\n \"G_4\": [\"M\", \"-M\", \"-D\"],\n \"G_6\": [\"1-M\", \"M\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"M\"],\n [\"M\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC3\": {\n kparam: [\n [\"Z\", \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\"],\n [\"R\", \"1-Zbb/a/a\"],\n [\"E\", \"1/2-2Zccosbeta/a\"],\n [\"F\", \"E/2+aa/4/b/b+accosbeta/2/b/b\"],\n [\"U\", \"2F-Z\"],\n [\"W\", \"c/2/a/cosbeta(1-4U+aasinbetasinbeta/b/b)\"],\n [\"D\", \"-1/4+W/2-Zccosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"I\": [\"-1+R\", \"R\", \"1/2\"],\n \"I_2\": [\"1-R\", \"1-R\", \"1/2\"],\n \"K\": [\"-U\", \"U\", \"W\"],\n \"K_2\": [\"-1+U\", \"1-U\", \"1-W\"],\n \"K_4\": [\"1-U\", \"U\", \"W\"],\n \"H\": [\"-Z\", \"Z\", \"E\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-E\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-E\"],\n \"N\": [\"-F\", \"F\", \"D\"],\n \"N_2\": [\"F\", \"1-F\", \"-D\"],\n \"N_4\": [\"F\", \"-F\", \"-D\"],\n \"N_6\": [\"1-F\", \"F\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"A\"],\n [\"A\", \"I_2\"],\n [\"I\", \"M_2\"],\n [\"M_2\", \"GAMMA\"],\n [\"GAMMA\", \"Y\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mP1\": {\n kparam: [\n [\"Y\", \"(1+a/ccosbeta)/2/sinbeta/sinbeta\"],\n [\"N\", \"1/2+Yccosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"1/2\", \"0\"],\n \"B\": [\"0\", \"0\", \"1/2\"],\n \"B_2\": [\"0\", \"0\", \"-1/2\"],\n \"Y\": [\"1/2\", 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\"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oA2\": {\n kparam: [\n [\"X\", \"(1+cc/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC1\": {\n kparam: [\n [\"X\", \"(1+aa/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"-1/2\", \"1/2\", \"0\"],\n \"T\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC2\": {\n kparam: [\n [\"X\", \"(1+bb/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oF1\": {\n kparam: [\n [\"J\", \"(1+aa/b/b-aa/c/c)/4\"],\n [\"H\", \"(1+aa/b/b+aa/c/c)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"SIGMA_0\": [\"0\", \"H\", \"H\"],\n \"U_0\": [\"1\", \"1-H\", \"1-H\"],\n \"A_0\": [\"1/2\", \"1/2+J\", \"J\"],\n \"C_0\": [\"1/2\", \"1/2-J\", \"1-J\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"GAMMA\"],\n [\"GAMMA\", \"SIGMA_0\"],\n [\"U_0\", \"T\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF2\": {\n kparam: [\n [\"J\", \"(1+cc/a/a-cc/b/b)/4\"],\n [\"K\", \"(1+cc/a/a+cc/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"1\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"LAMBDA_0\": [\"K\", \"K\", \"0\"],\n \"Q_0\": [\"1-K\", \"1-K\", \"1\"],\n \"G_0\": [\"1/2-J\", \"1-J\", \"1/2\"],\n \"H_0\": [\"1/2+J\", \"J\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"Q_0\", \"Z\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF3\": {\n kparam: [\n [\"H\", \"(1+aa/b/b-aa/c/c)/4\"],\n [\"K\", \"(1+bb/a/a-bb/c/c)/4\"],\n [\"P\", \"(1+cc/b/b-cc/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"A_0\": [\"1/2\", \"1/2+H\", \"H\"],\n \"C_0\": [\"1/2\", \"1/2-H\", \"1-H\"],\n \"B_0\": [\"1/2+K\", \"1/2\", \"K\"],\n \"D_0\": [\"1/2-K\", \"1/2\", \"1-K\"],\n \"G_0\": [\"P\", \"1/2+P\", \"1/2\"],\n \"H_0\": [\"1-P\", \"1/2-P\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"D_0\", \"T\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"T\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oI1\": {\n kparam: [\n [\"Z\", \"(1+aa/c/c)/4\"],\n [\"H\", \"(1+bb/c/c)/4\"],\n [\"D\", \"(bb-aa)/4/c/c\"],\n [\"N\", \"(aa+bb)/4/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Z\", \"Z\", \"Z\"],\n \"F_2\": [\"Z\", \"1-Z\", \"-Z\"],\n \"Y_0\": [\"H\", \"-H\", \"H\"],\n \"U_0\": [\"1-H\", \"H\", \"-H\"],\n \"L_0\": [\"-N\", \"N\", \"1/2-D\"],\n \"M_0\": [\"N\", \"-N\", \"1/2+D\"],\n \"J_0\": [\"1/2-D\", \"1/2+D\", \"-N\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_2\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Y_0\"],\n [\"U_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI2\": {\n kparam: [\n [\"Z\", \"(1+bb/a/a)/4\"],\n [\"H\", \"(1+cc/a/a)/4\"],\n [\"D\", \"(cc-bb)/4/a/a\"],\n [\"N\", \"(bb+cc)/4/a/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Y_0\": [\"Z\", \"-Z\", \"Z\"],\n \"U_2\": [\"-Z\", \"Z\", \"1-Z\"],\n \"LAMBDA_0\": [\"H\", \"H\", \"-H\"],\n \"G_2\": [\"-H\", \"1-H\", \"H\"],\n \"K\": [\"1/2-D\", \"-N\", \"N\"],\n \"K_2\": [\"1/2+D\", \"N\", \"-N\"],\n \"K_4\": [\"-N\", \"1/2-D\", \"1/2+D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U_2\"],\n [\"Y_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_2\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI3\": {\n kparam: [\n [\"Z\", \"(1+cc/b/b)/4\"],\n [\"Y\", \"(1+aa/b/b)/4\"],\n [\"D\", \"(aa-cc)/4/b/b\"],\n [\"M\", \"(cc+aa)/4/b/b\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Y\", \"Y\", \"Y\"],\n \"F_0\": [\"Y\", \"-Y\", \"1-Y\"],\n \"LAMBDA_0\": [\"Z\", \"Z\", \"-Z\"],\n \"G_0\": [\"1-Z\", \"-Z\", \"Z\"],\n \"V_0\": [\"M\", \"1/2-D\", \"-M\"],\n \"H_0\": [\"-M\", \"1/2+D\", \"M\"],\n \"H_2\": [\"1/2+D\", \"-M\", \"1/2-D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"S\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"S\"],\n [\"S\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"U\"],\n [\"U\", \"R\"],\n [\"R\", \"T\"],\n [\"T\", \"Z\"],\n [\"X\", \"U\"],\n [\"Y\", \"T\"],\n [\"S\", \"R\"]\n ],\n },\n \"tI1\": {\n kparam: [\n [\"H\", \"(1+cc/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Z\": [\"H\", \"H\", \"-H\"],\n \"Z_0\": [\"-H\", \"1-H\", \"H\"],\n \"N\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z_0\", \"M\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"]\n ],\n },\n \"tI2\": {\n kparam: [\n [\"H\", \"(1+aa/c/c)/4\"],\n [\"Z\", \"aa/2/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"1/2\", \"0\"],\n \"S_0\": [\"-H\", \"H\", \"H\"],\n \"S\": [\"H\", \"1-H\", \"-H\"],\n \"R\": [\"-Z\", \"Z\", \"1/2\"],\n \"G\": [\"1/2\", \"1/2\", \"-Z\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"M\"],\n [\"M\", \"S\"],\n [\"S_0\", \"GAMMA\"],\n [\"X\", \"R\"],\n [\"G\", \"M\"]\n ],\n },\n \"tP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"1/2\", \"1/2\", \"1/2\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"R\"],\n [\"R\", \"A\"],\n [\"A\", \"Z\"],\n [\"X\", \"R\"],\n [\"M\", \"A\"]\n ],\n },\n};\n\nexport const extBravaisLattices = Object.keys(bandPathData);\n","import type { MoyoDataset } from \"@spglib/moyo-wasm\";\nimport { Structure } from \"../../../structure\";\nimport { getSymmetry } from \"../spglib\";\nimport { spgroup_data } from \"../spgData\";\n\nimport { parameters } from \"../../../../lattice/parameters\";\n\nimport { determinant } from \"@/core/matrix/operations/determinant\";\nimport type { KPath } from \"@/core/kpoints\";\n\nimport { transformAP, determineExtBravais, determineAP } from \"./bravais\";\nimport {\n cellParams,\n evalExpr,\n evalExprSimple,\n extendKparam,\n getPmatrix,\n getPrimitive,\n getReciprocalCellRows,\n matrixFromRowMajor,\n vecMulMat,\n} from \"./seekpathTools\";\nimport { bandPathData } from \"./bandPathData\";\n\nconst RAD2DEG = 180 / Math.PI;\n\nfunction rowsFromFlat(data: ArrayLike<number>): number[][] {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return [\n [data[0], data[1], data[2]],\n [data[3], data[4], data[5]],\n [data[6], data[7], data[8]],\n ];\n}\n\n/* Compute [a, b, c, alphaDeg, betaDeg, gammaDeg] from a row-major 3x3 lattice. /\nfunction cellParamsDegrees(data: ArrayLike<number>): number[] {\n const [a, b, c, cosalpha, cosbeta, cosgamma] = cellParams(\n matrixFromRowMajor(data),\n );\n const acos = (x: number) => Math.acos(Math.max(-1, Math.min(1, x))) RAD2DEG;\n return [a, b, c, acos(cosalpha), acos(cosbeta), acos(cosgamma)];\n}\n\n/** Determine the Seekpath extended Bravais lattice from symmetry data. /\nexport async function getSeekPathHighSymPath(\n structure: Structure,\n symTol = 1e-6,\n): Promise<string> {\n const symData = await getSymmetry(structure, symTol);\n\n const conventionalLattice = symData.conventional.lattice;\n const [a, b, c, alpha, beta, gamma] = parameters(conventionalLattice);\n const spgN = symData.calculationResults.number;\n\n const props = spgroup_data[spgN];\n if (!props) throw new Error(`No space group data for SG ${spgN}`);\n const bL = `${props[0]}${props[1]}`;\n\n if (bL === \"aP\") {\n return determineAP(conventionalLattice.basis);\n }\n\n return determineExtBravais(bL, spgN, a, b, c, alpha, beta, gamma);\n}\n\nexport interface GetPathOptions {\n withTimeReversal?: boolean;\n threshold?: number;\n symprec?: number;\n}\n\nexport interface SeekPathResult {\n readonly kpath: KPath;\n point_coords: Record<string, [number, number, number]>;\n path: [string, string][];\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n bravais_lattice: string;\n bravais_lattice_extended: string;\n conv_lattice: number[][];\n conv_positions: number[][];\n conv_types: number[];\n primitive_lattice: number[][];\n primitive_positions: number[][];\n primitive_types: number[];\n reciprocal_primitive_lattice: number[][];\n inverse_primitive_transformation_matrix: number[][];\n primitive_transformation_matrix: number[][];\n volume_original_wrt_conv: number;\n volume_original_wrt_prim: number;\n spacegroup_number: number;\n spacegroup_international: string;\n rotation_matrix: number[][];\n}\n\n/\n Return the k-point path information for a band structure, following the\n * HPKOT recipe. Mirrors `seekpath.get_path`.\n /\nexport async function getPath(\n structure: Structure,\n opts: GetPathOptions = {},\n): Promise<SeekPathResult> {\n const {\n withTimeReversal = true,\n threshold = 1e-7,\n symprec = 1e-5,\n } = opts;\n\n const symData = await getSymmetry(structure, symprec);\n const calcResults: MoyoDataset = symData.calculationResults;\n\n const stdCell = calcResults.std_cell;\n const convLatticeFlat = stdCell.lattice.basis;\n const convPositions = stdCell.positions.map((p) => Array.from(p));\n const convTypes = Array.from(stdCell.numbers);\n\n const spgrpNum = calcResults.number;\n const properties = spgroup_data[spgrpNum];\n if (!properties) {\n throw new Error(`No space group data for SG ${spgrpNum}`);\n }\n const bravaisLattice = `${properties[0]}${properties[1]}`;\n const hasInv = properties[2];\n\n const [a, b, c, alphaDeg, betaDeg, gammaDeg] = cellParamsDegrees(\n convLatticeFlat,\n );\n\n // Implement all different extended Bravais lattices\n let extBravais: string;\n let convLattice: number[][];\n let convPositionsFinal: number[][];\n\n if (bravaisLattice === \"aP\") {\n const ap = await transformAP(rowsFromFlat(convLatticeFlat), convPositions);\n extBravais = ap.extBravais;\n convLattice = ap.lattice;\n convPositionsFinal = ap.positions;\n } else {\n extBravais = determineExtBravais(\n bravaisLattice,\n spgrpNum,\n a,\n b,\n c,\n alphaDeg,\n betaDeg,\n gammaDeg,\n );\n convLattice = rowsFromFlat(convLatticeFlat);\n convPositionsFinal = convPositions;\n }\n\n // Primitive cell from the conventional cell via the HPKOT P matrix\n const primitive = getPrimitive(\n convLattice,\n convPositionsFinal,\n convTypes,\n bravaisLattice,\n );\n const { P, invP } = getPmatrix(bravaisLattice);\n\n // Get the path data (k-parameters definitions, point definitions, path)\n const data = bandPathData[extBravais];\n if (!data) throw new Error(`No band path data for extended Bravais ${extBravais}`);\n\n const [kparamDef, pointsDef, basePath] = [\n data.kparam,\n data.points,\n data.path,\n ];\n\n const cosalpha = Math.cos(alphaDeg Math.PI / 180);\n const cosbeta = Math.cos(betaDeg * Math.PI / 180);\n const cosgamma = Math.cos(gammaDeg * Math.PI / 180);\n\n const kparam: Record<string, number> = {};\n for (const [kparamName, kparamExpr] of kparamDef) {\n kparam[kparamName] = evalExpr(\n kparamExpr,\n a,\n b,\n c,\n cosalpha,\n cosbeta,\n cosgamma,\n kparam,\n );\n }\n const kparamExtended = extendKparam(kparam);\n\n const points: Record<string, [number, number, number]> = {};\n for (const [pointName, coordsDef] of Object.entries(pointsDef)) {\n points[pointName] = coordsDef.map((e) =>\n evalExprSimple(e, kparamExtended),\n ) as [number, number, number];\n }\n\n // If there is no inversion symmetry nor time-reversal symmetry, add\n // additional -k points\n const augmentedPath = !hasInv && !withTimeReversal;\n\n let path: [string, string][] = basePath;\n if (augmentedPath) {\n const negPoints: Record<string, [number, number, number]> = {};\n for (const [pointName, coords] of Object.entries(points)) {\n if (pointName === \"GAMMA\") continue;\n negPoints[`${pointName}'`] = [-coords[0], -coords[1], -coords[2]];\n }\n Object.assign(points, negPoints);\n\n const oldPath = basePath;\n const newSegments: [string, string][] = [];\n for (const [startP, endP] of oldPath) {\n newSegments.push([\n startP === \"GAMMA\" ? startP : `${startP}'`,\n endP === \"GAMMA\" ? endP : `${endP}'`,\n ]);\n }\n path = [...basePath, ...newSegments];\n }\n\n const primitiveMatrix = matrixFromRowMajor(primitive.lattice.flat());\n const reciprocalPrimitive = getReciprocalCellRows(primitiveMatrix);\n\n const origDet = Math.abs(\n determinant(matrixFromRowMajor(Array.from(structure.lattice.basis.data))),\n );\n const convDet = Math.abs(determinant(matrixFromRowMajor(convLattice.flat())));\n const primDet = Math.abs(determinant(primitiveMatrix));\n\n return {\n kpath: { kind: \"path\", points, segments: path },\n point_coords: points,\n path,\n has_inversion_symmetry: hasInv,\n augmented_path: augmentedPath,\n bravais_lattice: bravaisLattice,\n bravais_lattice_extended: extBravais,\n conv_lattice: convLattice,\n conv_positions: convPositionsFinal,\n conv_types: convTypes,\n primitive_lattice: primitive.lattice,\n primitive_positions: primitive.positions,\n primitive_types: primitive.types,\n reciprocal_primitive_lattice: Array.from(reciprocalPrimitive.data).reduce<\n number[][]\n >(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n ),\n inverse_primitive_transformation_matrix: invP,\n primitive_transformation_matrix: P,\n volume_original_wrt_conv: origDet / convDet,\n volume_original_wrt_prim: origDet / primDet,\n spacegroup_number: spgrpNum,\n spacegroup_international: calcResults.hm_symbol,\n rotation_matrix: rowsFromFlat(calcResults.std_rotation_matrix),\n };\n}\n\nexport interface ExplicitKPathResult extends SeekPathResult {\n explicit_kpoints_abs: number[][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_labels: string[];\n explicit_kpoints_linearcoord: number[];\n explicit_segments: [number, number][];\n}\n\nfunction vecAdd(a: readonly number[], b: readonly number[]): number[] {\n return [a[0] + b[0], a[1] + b[1], a[2] + b[2]];\n}\n\nfunction vecSub(a: readonly number[], b: readonly number[]): number[] {\n return [a[0] - b[0], a[1] - b[1], a[2] - b[2]];\n}\n\nfunction vecScale(a: readonly number[], k: number): number[] {\n return [a[0] * k, a[1] * k, a[2] * k];\n}\n\nfunction vecNorm(a: readonly number[]): number {\n return Math.hypot(a[0], a[1], a[2]);\n}\n\n/*\n Given the output of `getPath`, compute an \"explicit\" path, i.e. a full list\n * of k-points along each segment. Mirrors `seekpath.get_explicit_from_implicit`.\n /\nexport function getExplicitFromImplicit(\n result: Pick<SeekPathResult, \"kpath\" \| \"reciprocal_primitive_lattice\">,\n referenceDistance = 0.025,\n): {\n kpoints_rel: number[][];\n kpoints_abs: number[][];\n kpoints_labels: string[];\n kpoints_linearcoord: number[];\n segments: [number, number][];\n} {\n const recip = result.reciprocal_primitive_lattice;\n\n const kpointsRel: number[][] = [];\n const kpointsLabels: string[] = [];\n const kpointsLinearcoord: number[] = [];\n const segments: [number, number][] = [];\n let previousLinearcoord = 0;\n\n for (const [startLabel, stopLabel] of result.kpath.segments) {\n const startCoord = result.kpath.points[startLabel];\n const stopCoord = result.kpath.points[stopLabel];\n const startCoordAbs = vecMulMat(startCoord, recip);\n const stopCoordAbs = vecMulMat(stopCoord, recip);\n const segmentLength = vecNorm(vecSub(stopCoordAbs, startCoordAbs));\n const numPoints = Math.max(2, Math.floor(segmentLength / referenceDistance));\n\n let segmentStart = kpointsLabels.length;\n for (let i = 0; i < numPoints; i++) {\n // Skip the first point if it's the same as the last one of the\n // previous segment\n if (i === 0) {\n if (\n kpointsLabels.length &&\n kpointsLabels[kpointsLabels.length - 1] === startLabel\n ) {\n segmentStart -= 1;\n continue;\n }\n }\n\n kpointsRel.push(\n vecAdd(startCoord, vecScale(vecSub(stopCoord, startCoord), i / (numPoints - 1))),\n );\n if (i === 0) kpointsLabels.push(startLabel);\n else if (i === numPoints - 1) kpointsLabels.push(stopLabel);\n else kpointsLabels.push(\"\");\n kpointsLinearcoord.push(\n previousLinearcoord + (segmentLength i) / (numPoints - 1),\n );\n }\n previousLinearcoord += segmentLength;\n segments.push([segmentStart, kpointsLabels.length]);\n }\n\n return {\n kpoints_rel: kpointsRel,\n kpoints_abs: kpointsRel.map((p) => vecMulMat(p, recip)),\n kpoints_labels: kpointsLabels,\n kpoints_linearcoord: kpointsLinearcoord,\n segments,\n };\n}\n\n/*\n Return the k-point path for a band structure in scaled and absolute\n * coordinates, following the HPKOT recipe. Mirrors\n * `seekpath.get_explicit_k_path`.\n /\nexport async function getExplicitKPath(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<ExplicitKPathResult> {\n const { referenceDistance = 0.025, ...rest } = opts;\n const res = await getPath(structure, rest);\n const explicit = getExplicitFromImplicit(res, referenceDistance);\n\n return {\n ...res,\n explicit_kpoints_abs: explicit.kpoints_abs,\n explicit_kpoints_rel: explicit.kpoints_rel,\n explicit_kpoints_labels: explicit.kpoints_labels,\n explicit_kpoints_linearcoord: explicit.kpoints_linearcoord,\n explicit_segments: explicit.segments,\n };\n}\n\n// re-export for convenience\nexport { bandPathData } from \"./bandPathData\";\n","import { Structure } from \"../../../structure\";\n\nimport { getExplicitKPath } from \"./seekpath\";\nimport type { GetPathOptions } from \"./seekpath\";\nimport { getBZPolyhedron } from \"./bzPolyhedron\";\nimport { vecMulMat } from \"./seekpathTools\";\nimport type { KPath } from \"@/core/kpoints\";\n\n/* Data object compatible with the `brillouinzone-visualizer` widget. /\nexport interface BZVisualizerData {\n b1: number[];\n b2: number[];\n b3: number[];\n faces_data: {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n };\n kpoints: Record<string, number[]>;\n kpoints_rel: Record<string, number[]>;\n /* The high-symmetry path, serializable via `toKPOINTS`. /\n kpath: KPath;\n path: [string, string][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_linearcoord: number[];\n explicit_kpoints_labels: string[];\n explicit_kpoints_abs: number[][];\n explicit_segments: [number, number][];\n bravais_lattice: string;\n bravais_lattice_extended: string;\n spacegroup_number: number;\n spacegroup_international: string;\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n}\n\n/\n Run the HPKOT high-symmetry path computation and assemble the data object\n * consumed by the `brillouinzone-visualizer` web widget, mirroring the\n * seekpath example-data generator.\n /\nexport async function getBrillouinZoneData(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<BZVisualizerData> {\n const res = await getExplicitKPath(structure, opts);\n\n const [b1, b2, b3] = res.reciprocal_primitive_lattice;\n const faces_data = getBZPolyhedron(b1, b2, b3);\n\n const kpoints: Record<string, number[]> = {};\n const kpoints_rel: Record<string, number[]> = {};\n for (const [label, rel] of Object.entries(res.kpath.points)) {\n kpoints_rel[label] = Array.from(rel);\n kpoints[label] = vecMulMat(rel, res.reciprocal_primitive_lattice);\n }\n\n return {\n b1,\n b2,\n b3,\n faces_data,\n kpoints,\n kpoints_rel,\n kpath: res.kpath,\n path: res.path,\n explicit_kpoints_rel: res.explicit_kpoints_rel,\n explicit_kpoints_linearcoord: res.explicit_kpoints_linearcoord,\n explicit_kpoints_labels: res.explicit_kpoints_labels,\n explicit_kpoints_abs: res.explicit_kpoints_abs,\n explicit_segments: res.explicit_segments,\n bravais_lattice: res.bravais_lattice,\n bravais_lattice_extended: res.bravais_lattice_extended,\n spacegroup_number: res.spacegroup_number,\n spacegroup_international: res.spacegroup_international,\n has_inversion_symmetry: res.has_inversion_symmetry,\n augmented_path: res.augmented_path,\n };\n}\n","/* Pauling electronegativity values keyed by element symbol. /\nexport const electronegativity: Record<string, number> = {\n Fr: 0.7,\n Cs: 0.79,\n Rb: 0.82,\n K: 0.82,\n Ba: 0.89,\n Ra: 0.9,\n Na: 0.93,\n Sr: 0.95,\n Li: 0.98,\n Ca: 1.0,\n Yb: 1.1,\n Eu: 1.2,\n Gd: 1.2,\n Tb: 1.1,\n La: 1.1,\n Ac: 1.1,\n Ce: 1.12,\n Pr: 1.13,\n Pm: 1.13,\n Am: 1.13,\n Nd: 1.14,\n Sm: 1.17,\n Dy: 1.22,\n Y: 1.22,\n Ho: 1.23,\n Er: 1.24,\n Tm: 1.25,\n Lu: 1.27,\n Cm: 1.28,\n Pu: 1.28,\n Np: 1.36,\n U: 1.38,\n Th: 1.3,\n Hf: 1.3,\n Zr: 1.33,\n Bk: 1.3,\n Cf: 1.3,\n Es: 1.3,\n Fm: 1.3,\n Md: 1.3,\n No: 1.3,\n Lr: 1.3,\n Pa: 1.5,\n Ta: 1.5,\n Ti: 1.54,\n Mn: 1.55,\n Mg: 1.31,\n Sc: 1.36,\n Be: 1.57,\n V: 1.63,\n Zn: 1.65,\n Cr: 1.66,\n Cd: 1.69,\n In: 1.78,\n Fe: 1.83,\n Co: 1.88,\n Ni: 1.91,\n Cu: 1.9,\n Ag: 1.93,\n Tl: 1.62,\n Nb: 1.6,\n Mo: 2.16,\n Tc: 1.9,\n Ru: 2.2,\n Rh: 2.28,\n Pd: 2.2,\n Sn: 1.96,\n Sb: 2.05,\n Te: 2.1,\n I: 2.66,\n Pt: 2.28,\n Au: 2.54,\n Hg: 2.0,\n Pb: 2.33,\n Bi: 2.02,\n Po: 2.0,\n At: 2.2,\n Ga: 1.81,\n Ge: 2.01,\n As: 2.18,\n Se: 2.55,\n Br: 2.96,\n Os: 2.2,\n Ir: 2.2,\n Re: 1.9,\n W: 2.36,\n Al: 1.61,\n Si: 1.9,\n P: 2.19,\n S: 2.58,\n Cl: 3.16,\n B: 2.04,\n C: 2.55,\n N: 3.04,\n O: 3.44,\n F: 3.98,\n H: 2.2,\n};\n","import { Structure } from \"../structure\";\nimport { gcd } from \"../../math/numeric\";\nimport { electronegativity } from \"../../data/periodictable/electronegativity\";\n\n/\n Count each element's occurrences in the structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to counts.\n /\nexport function composition(structure: Structure): Record<string, number> {\n const out: Record<string, number> = {};\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n out[symbol] ??= 0;\n out[symbol]++;\n }\n\n return out;\n}\n\nfunction compositionGCD(comp: Record<string, number>): number {\n const values = Object.values(comp);\n\n return values.reduce((a, b) => gcd(a, b));\n}\n\nfunction hillOrder(elements: string[]): string[] {\n if (!elements.includes(\"C\")) {\n return [...elements].sort();\n }\n\n const rest = elements.filter((e) => e !== \"C\" && e !== \"H\").sort();\n\n return [\"C\", ...(elements.includes(\"H\") ? [\"H\"] : []), ...rest];\n}\n\nfunction alphabeticalOrder(elements: string[]): string[] {\n return [...elements].sort();\n}\n\nfunction iupacOrder(elements: string[]): string[] {\n return [...elements].sort((a, b) => {\n const ea = electronegativity[a];\n const eb = electronegativity[b];\n\n if (ea === undefined && eb === undefined) return a.localeCompare(b);\n if (ea === undefined) return 1;\n if (eb === undefined) return -1;\n\n return ea - eb \|\| a.localeCompare(b);\n });\n}\n\nfunction formulaFromComposition(\n comp: Record<string, number>,\n ordering: (elements: string[]) => string[],\n): string {\n const elements = ordering(Object.keys(comp));\n\n return elements\n .map((el) => {\n const count = comp[el];\n\n return count === 1 ? el : `${el}${count}`;\n })\n .join(\"\");\n}\n\nexport function reducedComposition(\n comp: Record<string, number>,\n): Record<string, number> {\n const factor = compositionGCD(comp);\n\n const out: Record<string, number> = {};\n\n for (const [element, count] of Object.entries(comp)) {\n out[element] = count / factor;\n }\n\n return out;\n}\n\nconst SUBSCRIPT_DIGITS = [\"₀\", \"₁\", \"₂\", \"₃\", \"₄\", \"₅\", \"₆\", \"₇\", \"₈\", \"₉\"];\n\nconst SUBSCRIPT_TO_DIGIT: Record<string, string> = {\n \"₀\": \"0\",\n \"₁\": \"1\",\n \"₂\": \"2\",\n \"₃\": \"3\",\n \"₄\": \"4\",\n \"₅\": \"5\",\n \"₆\": \"6\",\n \"₇\": \"7\",\n \"₈\": \"8\",\n \"₉\": \"9\",\n};\n\n/* Label for anonymous formula ordering: 0 -> A, 25 -> Z, 26 -> AA, ... /\nfunction anonymousLabel(index: number): string {\n let out = \"\";\n let n = index;\n\n do {\n out = String.fromCharCode(65 + (n % 26)) + out;\n n = Math.floor(n / 26) - 1;\n } while (n >= 0);\n\n return out;\n}\n\nfunction formulaWithSubscripts(formula: string): string {\n return formula.replace(/\\d+/g, (digits) =>\n Array.from(digits, (d) => SUBSCRIPT_DIGITS[Number(d)]).join(\"\"),\n );\n}\n\nfunction anonymousFromComposition(comp: Record<string, number>): string {\n const entries = Object.entries(comp).sort(\n (a, b) => b[1] - a[1] \|\| a[0].localeCompare(b[0]),\n );\n\n return entries\n .map(([, count], i) => {\n const label = anonymousLabel(i);\n\n return count === 1 ? label : `${label}${count}`;\n })\n .join(\"\");\n}\n\nfunction mergeInto(\n target: Record<string, number>,\n source: Record<string, number>,\n multiplier: number,\n): void {\n for (const [element, count] of Object.entries(source)) {\n target[element] = (target[element] ?? 0) + count multiplier;\n }\n}\n\nfunction tokenizeFormula(text: string): string[] {\n const tokens: string[] = [];\n let i = 0;\n\n while (i < text.length) {\n const ch = text[i];\n\n if (/\\s/.test(ch)) {\n i++;\n } else if (\"()[]{}\".includes(ch)) {\n tokens.push(ch);\n i++;\n } else if (/[A-Z]/.test(ch)) {\n let j = i + 1;\n while (j < text.length && /[a-z]/.test(text[j])) j++;\n tokens.push(text.slice(i, j));\n i = j;\n } else if (/[0-9]/.test(ch)) {\n let j = i;\n while (j < text.length && /[0-9]/.test(text[j])) j++;\n\n if (text[j] === \".\" && /[0-9]/.test(text[j + 1] ?? \"\")) {\n j++;\n while (j < text.length && /[0-9]/.test(text[j])) j++;\n }\n\n tokens.push(text.slice(i, j));\n i = j;\n } else {\n throw new Error(`Invalid character '${ch}' in formula`);\n }\n }\n\n return tokens;\n}\n\nfunction assertBalanced(text: string): void {\n const pairs: Record<string, string> = { \"(\": \")\", \"[\": \"]\", \"{\": \"}\" };\n const stack: string[] = [];\n\n for (const ch of text) {\n if (ch === \"(\" \|\| ch === \"[\" \|\| ch === \"{\") {\n stack.push(ch);\n } else if (ch === \")\" \|\| ch === \"]\" \|\| ch === \"}\") {\n const top = stack.pop();\n\n if (top === undefined \|\| pairs[top] !== ch) {\n throw new Error(`Unbalanced brackets in formula: ${text}`);\n }\n }\n }\n\n if (stack.length > 0) {\n throw new Error(`Unbalanced brackets in formula: ${text}`);\n }\n}\n\nfunction parseTokens(tokens: string[]): Record<string, number> {\n let idx = 0;\n const isNumber = (tok: string): boolean => /^[0-9]/.test(tok);\n\n function readCount(): number {\n const tok = tokens[idx];\n\n if (tok !== undefined && isNumber(tok)) {\n idx++;\n return Number(tok);\n }\n\n return 1;\n }\n\n function parseGroup(): Record<string, number> {\n const comp: Record<string, number> = {};\n let leading = 1;\n\n if (idx < tokens.length && isNumber(tokens[idx])) {\n leading = Number(tokens[idx]);\n idx++;\n }\n\n while (idx < tokens.length) {\n const tok = tokens[idx];\n\n if (tok === \")\" \|\| tok === \"]\" \|\| tok === \"}\") break;\n\n if (tok === \"(\" \|\| tok === \"[\" \|\| tok === \"{\") {\n idx++;\n const inner = parseGroup();\n idx++;\n mergeInto(comp, inner, readCount());\n continue;\n }\n\n if (isNumber(tok)) {\n throw new Error(`Unexpected number '${tok}' in formula`);\n }\n\n const symbol = tok;\n idx++;\n comp[symbol] = (comp[symbol] ?? 0) + readCount();\n }\n\n if (leading !== 1) {\n for (const element of Object.keys(comp)) {\n comp[element] = leading;\n }\n }\n\n return comp;\n }\n\n const result: Record<string, number> = {};\n\n while (idx < tokens.length) {\n mergeInto(result, parseGroup(), 1);\n\n if (idx < tokens.length) {\n throw new Error(\"Unbalanced brackets in formula\");\n }\n }\n\n return result;\n}\n\n/\n Return the Hill-ordered chemical formula of a structure.\n * @param structure - Structure to evaluate.\n * @returns Hill-formula string.\n /\nexport function hillFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), hillOrder);\n}\n\n/\n Return the reduced Hill-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced formula string.\n /\nexport function reducedFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n );\n}\n\n/\n Return the alphabetically-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Alphabetical-formula string.\n /\nexport function alphabeticalFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), alphabeticalOrder);\n}\n\n/\n Return the reduced alphabetically-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced alphabetical-formula string.\n /\nexport function reducedAlphabeticalFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n alphabeticalOrder,\n );\n}\n\n/\n Return the IUPAC-ordered chemical formula (by increasing electronegativity).\n * @param structure - Structure to evaluate.\n * @returns IUPAC-formula string.\n /\nexport function iupacFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), iupacOrder);\n}\n\n/\n Return the reduced IUPAC-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced IUPAC-formula string.\n /\nexport function reducedIUPACFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n iupacOrder,\n );\n}\n\n/\n Return an anonymous formula where elements are labeled A, B, C, ...\n * by decreasing abundance.\n * @param structure - Structure to evaluate.\n * @returns Anonymous-formula string.\n /\nexport function anonymousFormula(structure: Structure): string {\n return anonymousFromComposition(composition(structure));\n}\n\n/\n Return the reduced anonymous formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced anonymous-formula string.\n /\nexport function reducedAnonymousFormula(structure: Structure): string {\n return anonymousFromComposition(reducedComposition(composition(structure)));\n}\n\n/\n Return the Hill-ordered formula with Unicode subscript digits.\n * @param structure - Structure to evaluate.\n * @returns Formula string with subscript digits.\n /\nexport function subscriptFormula(structure: Structure): string {\n return formulaWithSubscripts(\n formulaFromComposition(composition(structure), hillOrder),\n );\n}\n\n/\n Return the reduced Hill-ordered formula with Unicode subscript digits.\n * @param structure - Structure to evaluate.\n * @returns Reduced formula string with subscript digits.\n /\nexport function reducedSubscriptFormula(structure: Structure): string {\n return formulaWithSubscripts(\n formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n ),\n );\n}\n\n/\n Parse a chemical formula string into a composition.\n \n Supports element symbols, integer and decimal counts, nested bracket\n * groups (e.g. \"(NH4)2SO4\"), and dot/asterisk separated hydrate segments\n * (e.g. \"CaSO4·2H2O\" or \"CaSO42H2O\").\n @param text - Formula string to parse.\n * @returns Map of element symbols to counts.\n /\nexport function parseFormula(text: string): Record<string, number> {\n if (text.trim().length === 0) {\n throw new Error(\"Formula string is empty\");\n }\n\n const normalized = text.replace(/[₀-₉]/g, (ch) => SUBSCRIPT_TO_DIGIT[ch]);\n assertBalanced(normalized);\n\n const result: Record<string, number> = {};\n\n for (const segment of normalized.split(/[·]/)) {\n if (segment.length === 0) continue;\n\n mergeInto(result, parseTokens(tokenizeFormula(segment)), 1);\n }\n\n return result;\n}\n\n/*\n Count the total number of atoms (sites) in the structure.\n * @param structure - Structure to evaluate.\n * @returns Number of atoms.\n /\nexport function numAtoms(structure: Structure): number {\n return structure.sites.length;\n}\n","import type { Structure } from \"../../structure/structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nexport interface AssignmentResult {\n /* For each site i in A, the matched site index in B (or -1 if unassigned). /\n assignment: Int32Array;\n /* Per-site distances in the same order as A's sites. /\n distances: Float64Array;\n rms: number;\n maxDistance: number;\n}\n\n/* O(n^3) Hungarian (Kuhn–Munkres) solver for a square cost matrix.\n * Returns the column index assigned to each row. /\nfunction hungarian(cost: number[][]): number[] {\n const n = cost.length;\n const INF = Number.POSITIVE_INFINITY;\n\n const u = new Array<number>(n + 1).fill(0);\n const v = new Array<number>(n + 1).fill(0);\n const p = new Array<number>(n + 1).fill(0);\n const way = new Array<number>(n + 1).fill(0);\n\n for (let i = 1; i <= n; i++) {\n p[0] = i;\n let j0 = 0;\n const minv = new Array<number>(n + 1).fill(INF);\n const used = new Array<boolean>(n + 1).fill(false);\n\n do {\n used[j0] = true;\n const i0 = p[j0];\n let delta = INF;\n let j1 = -1;\n\n for (let j = 1; j <= n; j++) {\n if (!used[j]) {\n const cur = cost[i0 - 1][j - 1] - u[i0] - v[j];\n if (cur < minv[j]) {\n minv[j] = cur;\n way[j] = j0;\n }\n if (minv[j] < delta) {\n delta = minv[j];\n j1 = j;\n }\n }\n }\n\n for (let j = 0; j <= n; j++) {\n if (used[j]) {\n u[p[j]] += delta;\n v[j] -= delta;\n } else {\n minv[j] -= delta;\n }\n }\n\n j0 = j1;\n } while (p[j0] !== 0);\n\n do {\n const j1 = way[j0];\n p[j0] = p[j1];\n j0 = j1;\n } while (j0);\n }\n\n const result = new Array<number>(n);\n for (let j = 1; j <= n; j++) {\n result[p[j] - 1] = j - 1;\n }\n return result;\n}\n\n/* Group site indices by species symbol. /\nfunction groupBySpecies(structure: Structure): Map<string, number[]> {\n const groups = new Map<string, number[]>();\n structure.sites.forEach((site, index) => {\n const symbol = site.species.symbol;\n let list = groups.get(symbol);\n if (!list) {\n list = [];\n groups.set(symbol, list);\n }\n list.push(index);\n });\n return groups;\n}\n\n/\n Squared minimum-image distance between two fractional coordinates in the\n * lattice described by the metric tensor `G` (row-major 3x3). For non-orthogonal\n * lattices the true nearest image is found by searching small integer shifts.\n /\nfunction squaredMinimumImageDistance(\n fa: Float64Array,\n fb: Float64Array,\n G: Float64Array,\n): number {\n const dx = fb[0] - fa[0];\n const dy = fb[1] - fa[1];\n const dz = fb[2] - fa[2];\n\n let best = Number.POSITIVE_INFINITY;\n\n for (let i = -1; i <= 1; i++) {\n const x = dx - i;\n for (let j = -1; j <= 1; j++) {\n const y = dy - j;\n for (let k = -1; k <= 1; k++) {\n const z = dz - k;\n const d =\n x (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z);\n if (d < best) best = d;\n }\n }\n }\n\n return best < 0 ? 0 : best;\n}\n\n/*\n Find the optimal (minimum sum-of-squared distance) assignment of the sites of\n * `structureA` onto those of `structureB`, constrained so that matched sites\n * share the same species.\n \n Distances use the minimum-image convention in `structureA`'s metric, which\n * implicitly accounts for any lattice translation.\n \n Returns `null` when no species-valid complete assignment exists (i.e. the two\n * structures do not contain the same multiset of species).\n /\nexport function assignSites(\n structureA: Structure,\n structureB: Structure,\n maxPairDistance?: number,\n): AssignmentResult \| null {\n const groupsA = groupBySpecies(structureA);\n const groupsB = groupBySpecies(structureB);\n\n for (const [symbol, indicesA] of groupsA) {\n const indicesB = groupsB.get(symbol);\n if (!indicesB \|\| indicesB.length !== indicesA.length) {\n return null;\n }\n }\n\n const n = structureA.sites.length;\n const assignment = new Int32Array(n).fill(-1);\n const distances = new Float64Array(n);\n const G = metricTensor(structureA.lattice).data;\n\n const fracA = structureA.sites.map((site) => site.frac);\n const fracB = structureB.sites.map((site) => site.frac);\n\n const capSq =\n maxPairDistance !== undefined ? maxPairDistance maxPairDistance : Number.POSITIVE_INFINITY;\n\n let sumSquared = 0;\n let maxDist = 0;\n\n for (const [symbol, indicesA] of groupsA) {\n const indicesB = groupsB.get(symbol)!;\n const m = indicesA.length;\n\n if (m === 0) continue;\n\n const cost: number[][] = Array.from({ length: m }, () =>\n new Array<number>(m).fill(0),\n );\n\n for (let i = 0; i < m; i++) {\n const a = fracA[indicesA[i]];\n for (let j = 0; j < m; j++) {\n const b = fracB[indicesB[j]];\n const d = squaredMinimumImageDistance(a, b, G);\n cost[i][j] =\n capSq !== Number.POSITIVE_INFINITY && d > capSq\n ? Number.POSITIVE_INFINITY\n : d;\n }\n }\n\n // If any site has no partner within tolerance, no assignment within\n // tolerance is possible — skip the O(n³) Hungarian solver entirely.\n for (let i = 0; i < m; i++) {\n let feasible = false;\n for (let j = 0; j < m; j++) {\n if (cost[i][j] !== Number.POSITIVE_INFINITY) {\n feasible = true;\n break;\n }\n }\n if (!feasible) return null;\n }\n for (let j = 0; j < m; j++) {\n let feasible = false;\n for (let i = 0; i < m; i++) {\n if (cost[i][j] !== Number.POSITIVE_INFINITY) {\n feasible = true;\n break;\n }\n }\n if (!feasible) return null;\n }\n\n // Replace any remaining infinities with a huge finite cost so the solver\n // (which assumes finite costs) completes safely for the rare infeasible\n // case not caught above (a Hall violation). Such a match is rejected by the\n // rms check downstream.\n const BIG = 1e18;\n for (let i = 0; i < m; i++) {\n for (let j = 0; j < m; j++) {\n if (cost[i][j] === Number.POSITIVE_INFINITY) cost[i][j] = BIG;\n }\n }\n\n const perm = hungarian(cost);\n\n for (let i = 0; i < m; i++) {\n const aIndex = indicesA[i];\n const bIndex = indicesB[perm[i]];\n const distance = Math.sqrt(cost[i][perm[i]]);\n assignment[aIndex] = bIndex;\n distances[aIndex] = distance;\n sumSquared += distance * distance;\n if (distance > maxDist) maxDist = distance;\n }\n }\n\n const rms = n > 0 ? Math.sqrt(sumSquared / n) : 0;\n\n return { assignment, distances, rms, maxDistance: maxDist };\n}\n","import { Structure } from \"../../structure/structure\";\nimport { composition } from \"../../properties/formula\";\nimport { gcd } from \"../../../math/numeric\";\nimport { canonicalize } from \"../canonicalize\";\nimport { getSymmetry } from \"./spglib\";\nimport { assignSites } from \"./assign\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\n\nexport interface StructureMatchResult {\n matches: boolean;\n rms: number \| null;\n maxDistance: number \| null;\n distances: Float64Array \| null;\n}\n\ninterface SiteMatch {\n rms: number;\n maxDistance: number;\n distances: Float64Array;\n}\n\nfunction reducedComposition(\n comp: Record<string, number>,\n): Record<string, number> {\n const counts = Object.values(comp);\n\n if (counts.length === 0) {\n return {};\n }\n\n const factor = counts.reduce((a, b) => gcd(a, b));\n const reduced: Record<string, number> = {};\n\n for (const [element, count] of Object.entries(comp)) {\n reduced[element] = count / factor;\n }\n\n return reduced;\n}\n\nfunction sameComposition(\n compA: Record<string, number>,\n compB: Record<string, number>,\n): boolean {\n const elementsA = Object.keys(compA).sort();\n const elementsB = Object.keys(compB).sort();\n\n if (elementsA.length !== elementsB.length) {\n return false;\n }\n\n return elementsA.every(\n (element, index) =>\n element === elementsB[index] && compA[element] === compB[element],\n );\n}\n\nfunction noMatch(): StructureMatchResult {\n return {\n matches: false,\n rms: null,\n maxDistance: null,\n distances: null,\n };\n}\n\nfunction wrapComponent(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < 1e-12 ? 0 : v;\n}\n\n/** Apply a symmetry operation (rotation + translation, in fractional lattice\n * coordinates) to a structure's sites, keeping its lattice unchanged. /\nfunction applySymmetryOperation(\n structure: Structure,\n rotation: number[],\n translation: number[],\n): Structure {\n const sites = structure.sites.map((site) => {\n const f = site.frac;\n const x =\n rotation[0] f[0] +\n rotation[1] * f[1] +\n rotation[2] * f[2] +\n translation[0];\n const y =\n rotation[3] * f[0] +\n rotation[4] * f[1] +\n rotation[5] * f[2] +\n translation[1];\n const z =\n rotation[6] * f[0] +\n rotation[7] * f[1] +\n rotation[8] * f[2] +\n translation[2];\n\n return {\n ...site,\n frac: new Float64Array([\n wrapComponent(x),\n wrapComponent(y),\n wrapComponent(z),\n ]),\n };\n });\n\n return { ...structure, sites };\n}\n\n/** Apply a constant fractional translation to a structure's sites. /\nfunction translateStructure(\n structure: Structure,\n translation: number[],\n): Structure {\n return {\n ...structure,\n sites: structure.sites.map((site) => {\n const f = site.frac;\n return {\n ...site,\n frac: new Float64Array([\n wrapComponent(f[0] + translation[0]),\n wrapComponent(f[1] + translation[1]),\n wrapComponent(f[2] + translation[2]),\n ]),\n };\n }),\n };\n}\n\n/\n Distinct global translations that could align `candidate` onto `a`.\n \n Anchors a site belonging to the least-common shared species in `a` and\n * aligns it to every same-species site in `candidate`. The true alignment is\n * always recovered by one of these translations, while choosing the rarest\n * shared species minimizes the number of candidates that must be tested.\n /\nfunction candidateTranslations(a: Structure, candidate: Structure): number[][] {\n const candidateSpecies = new Set(\n candidate.sites.map((site) => site.species.symbol),\n );\n\n // Pick the shared species with the fewest sites in `a`.\n const counts = new Map<string, number>();\n\n for (const site of a.sites) {\n const symbol = site.species.symbol;\n\n if (candidateSpecies.has(symbol)) {\n counts.set(symbol, (counts.get(symbol) ?? 0) + 1);\n }\n }\n\n let anchorSpecies = \"\";\n let anchorCount = Infinity;\n\n for (const [symbol, count] of counts) {\n if (count < anchorCount) {\n anchorSpecies = symbol;\n anchorCount = count;\n }\n }\n\n if (!anchorSpecies) return [];\n\n const anchorIndex = a.sites.findIndex(\n (site) => site.species.symbol === anchorSpecies,\n );\n\n if (anchorIndex < 0) return [];\n\n const fa = a.sites[anchorIndex].frac;\n const seen = new Set<string>();\n const out: number[][] = [];\n\n for (const site of candidate.sites) {\n if (site.species.symbol !== anchorSpecies) continue;\n\n const fb = site.frac;\n\n const t = [\n wrapComponent(fa[0] - fb[0]),\n wrapComponent(fa[1] - fb[1]),\n wrapComponent(fa[2] - fb[2]),\n ];\n\n const key = `${t[0].toFixed(4)},${t[1].toFixed(4)},${t[2].toFixed(4)}`;\n\n if (!seen.has(key)) {\n seen.add(key);\n out.push(t);\n }\n }\n\n return out;\n}\n\n/* The 6 lattice-vector permutation matrices (row permutations). /\nfunction latticePermutations(): Matrix[] {\n const perms: number[][] = [\n [0, 1, 2],\n [0, 2, 1],\n [1, 0, 2],\n [1, 2, 0],\n [2, 0, 1],\n [2, 1, 0],\n ];\n\n return perms.map((perm) => {\n const data = new Float64Array(9);\n for (let r = 0; r < 3; r++) {\n data[r 3 + perm[r]] = 1;\n }\n return createMatrix(3, 3, data);\n });\n}\n\n/*\n All integer rotation matrices (entries in {-1, 0, 1}, determinant ±1) that\n * preserve the lattice metric `G`. This is the full lattice point group — a\n * superset of the space-group rotations returned by symmetry analysis and\n * robust to the basis/origin choices made by cell standardization.\n /\nfunction latticePointGroup(G: Float64Array): number[][] {\n const values = [-1, 0, 1];\n const out: number[][] = [];\n\n for (let idx = 0; idx < 19683; idx++) {\n const M = new Array<number>(9);\n let x = idx;\n for (let k = 0; k < 9; k++) {\n M[k] = values[x % 3];\n x = Math.floor(x / 3);\n }\n\n const det =\n M[0] (M[4] * M[8] - M[5] * M[7]) -\n M[1] * (M[3] * M[8] - M[5] * M[6]) +\n M[2] * (M[3] * M[7] - M[4] * M[6]);\n\n if (det !== 1 && det !== -1) continue;\n\n let preserves = true;\n for (let r = 0; r < 3 && preserves; r++) {\n for (let c = 0; c < 3; c++) {\n let s = 0;\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n s += M[r * 3 + i] * G[i * 3 + j] * M[c * 3 + j];\n }\n }\n if (Math.abs(s - G[r * 3 + c]) > 1e-6) {\n preserves = false;\n break;\n }\n }\n }\n\n if (preserves) out.push(M);\n }\n\n return out;\n}\n\n/*\n Match two structures using symmetry-normalized primitive cells, mirroring the\n * behaviour of pymatgen's `StructureMatcher` (primitive-cell matching with\n * symmetry-operation search and RMS tolerance).\n /\nexport async function matchStructures(\n structureA: Structure,\n structureB: Structure,\n tolerance = 0.3,\n symprec = 1e-4,\n): Promise<StructureMatchResult> {\n const reducedA = reducedComposition(composition(structureA));\n const reducedB = reducedComposition(composition(structureB));\n\n if (!sameComposition(reducedA, reducedB)) {\n return noMatch();\n }\n\n const [symmetryA, symmetryB] = await Promise.all([\n getSymmetry(structureA, symprec),\n getSymmetry(structureB, symprec),\n ]);\n\n const a = canonicalize(symmetryA.primitive);\n const b = canonicalize(symmetryB.primitive);\n\n if (a.sites.length !== b.sites.length) {\n return noMatch();\n }\n\n if (a.sites.length === 0) {\n return {\n matches: true,\n rms: 0,\n maxDistance: 0,\n distances: new Float64Array(),\n };\n }\n\n // Candidate rotations: the full lattice point group of `a` (rotations that\n // preserve its metric). This covers all symmetry-equivalent placements of `b`\n // within `a`'s frame, regardless of the basis/origin choice made during\n // standardization.\n const G = metricTensor(a.lattice).data;\n const rotations = latticePointGroup(G);\n const permutations = latticePermutations();\n\n let best: SiteMatch \| null = null;\n\n const consider = (candidate: Structure) => {\n const result = assignSites(a, candidate, tolerance);\n if (result === null) return;\n if (best === null \|\| result.rms < best.rms) {\n best = {\n rms: result.rms,\n maxDistance: result.maxDistance,\n distances: result.distances,\n };\n }\n };\n\n const evaluate = (candidate: Structure): boolean => {\n // Direct placement (no extra translation) — resolves well-behaved cases.\n consider(candidate);\n if (best !== null && best.rms <= tolerance) return true;\n\n // Search the global translation that aligns the two (handles origin-choice\n // differences between standardized primitives).\n for (const t of candidateTranslations(a, candidate)) {\n consider(translateStructure(candidate, t));\n if (best !== null && best.rms <= tolerance) return true;\n }\n\n return false;\n };\n\n // Iterate over lattice-vector relabellings of `b` (covers basis-ordering\n // choices) combined with every lattice point-group rotation.\n for (let p = 0; p < permutations.length; p++) {\n const bPerm = p === 0 ? b : applyTransformationBasis(b, permutations[p]);\n\n for (const rotation of rotations) {\n if (evaluate(applySymmetryOperation(bPerm, rotation, [0, 0, 0]))) {\n return {\n matches: true,\n rms: best!.rms,\n maxDistance: best!.maxDistance,\n distances: best!.distances,\n };\n }\n }\n }\n\n if (best === null) {\n return noMatch();\n }\n\n return {\n matches: best.rms <= tolerance,\n rms: best.rms,\n maxDistance: best.maxDistance,\n distances: best.distances,\n };\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Minimum-image distance between two sites. /\nexport function getDistance(\n structure: Structure,\n idx1: number,\n idx2: number,\n): number {\n const displacement = getDisplacement(structure, idx1, idx2);\n\n const G = metricTensor(structure.lattice).data;\n\n return Math.sqrt(distanceSquared(displacement, G));\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Distances from site `idx` to every other site. /\nexport function getDistances(structure: Structure, idx: number): Float64Array {\n const n = structure.sites.length;\n const out = new Float64Array(n);\n\n const G = metricTensor(structure.lattice).data;\n\n for (let j = 0; j < n; j++) {\n if (j === idx) {\n out[j] = 0;\n continue;\n }\n\n const disp = getDisplacement(structure, idx, j);\n\n out[j] = Math.sqrt(distanceSquared(disp, G));\n }\n\n return out;\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Pairwise distance matrix for all sites, stored as an array of Float64Array rows. /\nexport function getDistancesMatrix(structure: Structure): Float64Array[] {\n const n = structure.sites.length;\n\n const matrix: Float64Array[] = Array.from(\n { length: n },\n () => new Float64Array(n),\n );\n\n const G = metricTensor(structure.lattice).data;\n\n for (let i = 0; i < n; i++) {\n matrix[i][i] = 0;\n\n for (let j = i + 1; j < n; j++) {\n const disp = getDisplacement(structure, i, j);\n\n const d = Math.sqrt(distanceSquared(disp, G));\n\n matrix[i][j] = d;\n matrix[j][i] = d;\n }\n }\n\n return matrix;\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n// generic method for finding sites on a given condition.\n\n/* Find site indices matching a predicate. /\nexport function findSites(\n structure: Structure,\n predicate: (site: Site, index: number) => boolean,\n): number[] {\n const indices: number[] = [];\n\n for (let i = 0; i < structure.sites.length; i++) {\n if (predicate(structure.sites[i], i)) {\n indices.push(i);\n }\n }\n\n return indices;\n}\n","import { Species } from \"../../../species/species\";\nimport { Structure } from \"../../structure\";\nimport { findSites } from \"./findSites\";\n\n// matches species.symbol only.\n\n/* Find site indices whose species symbol matches the given species or string. /\nexport function findSitesBySpecies(\n structure: Structure,\n species: Species \| string,\n): number[] {\n const symbol = typeof species === \"string\" ? species : species.symbol;\n\n return findSites(structure, (site) => site.species.symbol === symbol);\n}\n","import { determinant } from \"../matrix/operations/determinant\";\nimport { Lattice } from \"./lattice\";\n\n/* Compute the unit cell volume as the absolute determinant of the basis. /\nexport function volume(lattice: Lattice): number {\n return Math.abs(determinant(lattice.basis));\n}\n","import { Structure } from \"../structure\";\nimport { volume as latticeVolume } from \"../../lattice/volume\";\n\n/\n Compute the volume of a structure's lattice cell.\n * @param structure - Structure to evaluate.\n * @returns Volume in Ang^3.\n /\nexport function volume(structure: Structure): number {\n return latticeVolume(structure.lattice);\n}\n","// NOTE: DISCUSS IF THIS THIS SHOULD BE ALL BUNDLED IN THE mc-periodic-table package.\n// WE CAN REEXPORT FROM THERE,\n\n/* Element metadata from the periodic table. /\nexport interface ElementInfo {\n atomicNumber: number;\n symbol: string;\n name: string;\n mass: number;\n [key: string]: unknown;\n}\n\n/* Atomic-number-keyed periodic table of all known elements. /\nexport const PeriodicTable: Record<number, ElementInfo> = {\n 1: { atomicNumber: 1, symbol: \"H\", name: \"Hydrogen\", mass: 1.008 },\n 2: { atomicNumber: 2, symbol: \"He\", name: \"Helium\", mass: 4.0026 },\n 3: { atomicNumber: 3, symbol: \"Li\", name: \"Lithium\", mass: 6.94 },\n 4: { atomicNumber: 4, symbol: \"Be\", name: \"Beryllium\", mass: 9.0122 },\n 5: { atomicNumber: 5, symbol: \"B\", name: \"Boron\", mass: 10.81 },\n 6: { atomicNumber: 6, symbol: \"C\", name: \"Carbon\", mass: 12.011 },\n 7: { atomicNumber: 7, symbol: \"N\", name: \"Nitrogen\", mass: 14.007 },\n 8: { atomicNumber: 8, symbol: \"O\", name: \"Oxygen\", mass: 15.999 },\n 9: { atomicNumber: 9, symbol: \"F\", name: \"Fluorine\", mass: 18.998 },\n 10: { atomicNumber: 10, symbol: \"Ne\", name: \"Neon\", mass: 20.18 },\n 11: { atomicNumber: 11, symbol: \"Na\", name: \"Sodium\", mass: 22.99 },\n 12: { atomicNumber: 12, symbol: \"Mg\", name: \"Magnesium\", mass: 24.305 },\n 13: { atomicNumber: 13, symbol: \"Al\", name: \"Aluminum\", mass: 26.982 },\n 14: { atomicNumber: 14, symbol: \"Si\", name: \"Silicon\", mass: 28.085 },\n 15: { atomicNumber: 15, symbol: \"P\", name: \"Phosphorus\", mass: 30.974 },\n 16: { atomicNumber: 16, symbol: \"S\", name: \"Sulfur\", mass: 32.06 },\n 17: { atomicNumber: 17, symbol: \"Cl\", name: \"Chlorine\", mass: 35.45 },\n 18: { atomicNumber: 18, symbol: \"Ar\", name: \"Argon\", mass: 39.948 },\n 19: { atomicNumber: 19, symbol: \"K\", name: \"Potassium\", mass: 39.098 },\n 20: { atomicNumber: 20, symbol: \"Ca\", name: \"Calcium\", mass: 40.078 },\n 21: { atomicNumber: 21, symbol: \"Sc\", name: \"Scandium\", mass: 44.956 },\n 22: { atomicNumber: 22, symbol: \"Ti\", name: \"Titanium\", mass: 47.867 },\n 23: { atomicNumber: 23, symbol: \"V\", name: \"Vanadium\", mass: 50.942 },\n 24: { atomicNumber: 24, symbol: \"Cr\", name: \"Chromium\", mass: 51.996 },\n 25: { atomicNumber: 25, symbol: \"Mn\", name: \"Manganese\", mass: 54.938 },\n 26: { atomicNumber: 26, symbol: \"Fe\", name: \"Iron\", mass: 55.845 },\n 27: { atomicNumber: 27, symbol: \"Co\", name: \"Cobalt\", mass: 58.933 },\n 28: { atomicNumber: 28, symbol: \"Ni\", name: \"Nickel\", mass: 58.693 },\n 29: { atomicNumber: 29, symbol: \"Cu\", name: \"Copper\", mass: 63.546 },\n 30: { atomicNumber: 30, symbol: \"Zn\", name: \"Zinc\", mass: 65.38 },\n 31: { atomicNumber: 31, symbol: \"Ga\", name: \"Gallium\", mass: 69.723 },\n 32: { atomicNumber: 32, symbol: \"Ge\", name: \"Germanium\", mass: 72.63 },\n 33: { atomicNumber: 33, symbol: \"As\", name: \"Arsenic\", mass: 74.922 },\n 34: { atomicNumber: 34, symbol: \"Se\", name: \"Selenium\", mass: 78.971 },\n 35: { atomicNumber: 35, symbol: \"Br\", name: \"Bromine\", mass: 79.904 },\n 36: { atomicNumber: 36, symbol: \"Kr\", name: \"Krypton\", mass: 83.798 },\n 37: { atomicNumber: 37, symbol: \"Rb\", name: \"Rubidium\", mass: 85.468 },\n 38: { atomicNumber: 38, symbol: \"Sr\", name: \"Strontium\", mass: 87.62 },\n 39: { atomicNumber: 39, symbol: \"Y\", name: \"Yttrium\", mass: 88.906 },\n 40: { atomicNumber: 40, symbol: \"Zr\", name: \"Zirconium\", mass: 91.224 },\n 41: { atomicNumber: 41, symbol: \"Nb\", name: \"Niobium\", mass: 92.906 },\n 42: { atomicNumber: 42, symbol: \"Mo\", name: \"Molybdenum\", mass: 95.95 },\n 43: { atomicNumber: 43, symbol: \"Tc\", name: \"Technetium\", mass: 98 },\n 44: { atomicNumber: 44, symbol: \"Ru\", name: \"Ruthenium\", mass: 101.07 },\n 45: { atomicNumber: 45, symbol: \"Rh\", name: \"Rhodium\", mass: 102.91 },\n 46: { atomicNumber: 46, symbol: \"Pd\", name: \"Palladium\", mass: 106.42 },\n 47: { atomicNumber: 47, symbol: \"Ag\", name: \"Silver\", mass: 107.868 },\n 48: { atomicNumber: 48, symbol: \"Cd\", name: \"Cadmium\", mass: 112.414 },\n 49: { atomicNumber: 49, symbol: \"In\", name: \"Indium\", mass: 114.818 },\n 50: { atomicNumber: 50, symbol: \"Sn\", name: \"Tin\", mass: 118.71 },\n 51: { atomicNumber: 51, symbol: \"Sb\", name: \"Antimony\", mass: 121.76 },\n 52: { atomicNumber: 52, symbol: \"Te\", name: \"Tellurium\", mass: 127.6 },\n 53: { atomicNumber: 53, symbol: \"I\", name: \"Iodine\", mass: 126.904 },\n 54: { atomicNumber: 54, symbol: \"Xe\", name: \"Xenon\", mass: 131.293 },\n 55: { atomicNumber: 55, symbol: \"Cs\", name: \"Cesium\", mass: 132.905 },\n 56: { atomicNumber: 56, symbol: \"Ba\", name: \"Barium\", mass: 137.33 },\n 57: { atomicNumber: 57, symbol: \"La\", name: \"Lanthanum\", mass: 138.905 },\n 58: { atomicNumber: 58, symbol: \"Ce\", name: \"Cerium\", mass: 140.12 },\n 59: { atomicNumber: 59, symbol: \"Pr\", name: \"Praseodymium\", mass: 140.91 },\n 60: { atomicNumber: 60, symbol: \"Nd\", name: \"Neodymium\", mass: 144.24 },\n 61: { atomicNumber: 61, symbol: \"Pm\", name: \"Promethium\", mass: 145 },\n 62: { atomicNumber: 62, symbol: \"Sm\", name: \"Samarium\", mass: 150.36 },\n 63: { atomicNumber: 63, symbol: \"Eu\", name: \"Europium\", mass: 151.964 },\n 64: { atomicNumber: 64, symbol: \"Gd\", name: \"Gadolinium\", mass: 157.25 },\n 65: { atomicNumber: 65, symbol: \"Tb\", name: \"Terbium\", mass: 158.93 },\n 66: { atomicNumber: 66, symbol: \"Dy\", name: \"Dysprosium\", mass: 162.5 },\n 67: { atomicNumber: 67, symbol: \"Ho\", name: \"Holmium\", mass: 164.93 },\n 68: { atomicNumber: 68, symbol: \"Er\", name: \"Erbium\", mass: 167.26 },\n 69: { atomicNumber: 69, symbol: \"Tm\", name: \"Thulium\", mass: 168.93 },\n 70: { atomicNumber: 70, symbol: \"Yb\", name: \"Ytterbium\", mass: 173.05 },\n 71: { atomicNumber: 71, symbol: \"Lu\", name: \"Lutetium\", mass: 174.97 },\n 72: { atomicNumber: 72, symbol: \"Hf\", name: \"Hafnium\", mass: 178.49 },\n 73: { atomicNumber: 73, symbol: \"Ta\", name: \"Tantalum\", mass: 180.95 },\n 74: { atomicNumber: 74, symbol: \"W\", name: \"Tungsten\", mass: 183.84 },\n 75: { atomicNumber: 75, symbol: \"Re\", name: \"Rhenium\", mass: 186.207 },\n 76: { atomicNumber: 76, symbol: \"Os\", name: \"Osmium\", mass: 190.23 },\n 77: { atomicNumber: 77, symbol: \"Ir\", name: \"Iridium\", mass: 192.217 },\n 78: { atomicNumber: 78, symbol: \"Pt\", name: \"Platinum\", mass: 195.084 },\n 79: { atomicNumber: 79, symbol: \"Au\", name: \"Gold\", mass: 196.967 },\n 80: { atomicNumber: 80, symbol: \"Hg\", name: \"Mercury\", mass: 200.592 },\n 81: { atomicNumber: 81, symbol: \"Tl\", name: \"Thallium\", mass: 204.38 },\n 82: { atomicNumber: 82, symbol: \"Pb\", name: \"Lead\", mass: 207.2 },\n 83: { atomicNumber: 83, symbol: \"Bi\", name: \"Bismuth\", mass: 208.98 },\n 84: { atomicNumber: 84, symbol: \"Po\", name: \"Polonium\", mass: 209 },\n 85: { atomicNumber: 85, symbol: \"At\", name: \"Astatine\", mass: 210 },\n 86: { atomicNumber: 86, symbol: \"Rn\", name: \"Radon\", mass: 222 },\n 87: { atomicNumber: 87, symbol: \"Fr\", name: \"Francium\", mass: 223 },\n 88: { atomicNumber: 88, symbol: \"Ra\", name: \"Radium\", mass: 226 },\n 89: { atomicNumber: 89, symbol: \"Ac\", name: \"Actinium\", mass: 227 },\n 90: { atomicNumber: 90, symbol: \"Th\", name: \"Thorium\", mass: 232.04 },\n 91: { atomicNumber: 91, symbol: \"Pa\", name: \"Protactinium\", mass: 231.04 },\n 92: { atomicNumber: 92, symbol: \"U\", name: \"Uranium\", mass: 238.03 },\n 93: { atomicNumber: 93, symbol: \"Np\", name: \"Neptunium\", mass: 237 },\n 94: { atomicNumber: 94, symbol: \"Pu\", name: \"Plutonium\", mass: 244 },\n 95: { atomicNumber: 95, symbol: \"Am\", name: \"Americium\", mass: 243 },\n 96: { atomicNumber: 96, symbol: \"Cm\", name: \"Curium\", mass: 247 },\n 97: { atomicNumber: 97, symbol: \"Bk\", name: \"Berkelium\", mass: 247 },\n 98: { atomicNumber: 98, symbol: \"Cf\", name: \"Californium\", mass: 251 },\n 99: { atomicNumber: 99, symbol: \"Es\", name: \"Einsteinium\", mass: 252 },\n 100: { atomicNumber: 100, symbol: \"Fm\", name: \"Fermium\", mass: 257 },\n 101: { atomicNumber: 101, symbol: \"Md\", name: \"Mendelevium\", mass: 258 },\n 102: { atomicNumber: 102, symbol: \"No\", name: \"Nobelium\", mass: 259 },\n 103: { atomicNumber: 103, symbol: \"Lr\", name: \"Lawrencium\", mass: 262 },\n 104: { atomicNumber: 104, symbol: \"Rf\", name: \"Rutherfordium\", mass: 267 },\n 105: { atomicNumber: 105, symbol: \"Db\", name: \"Dubnium\", mass: 270 },\n 106: { atomicNumber: 106, symbol: \"Sg\", name: \"Seaborgium\", mass: 269 },\n 107: { atomicNumber: 107, symbol: \"Bh\", name: \"Bohrium\", mass: 270 },\n 108: { atomicNumber: 108, symbol: \"Hs\", name: \"Hassium\", mass: 277 },\n 109: { atomicNumber: 109, symbol: \"Mt\", name: \"Meitnerium\", mass: 278 },\n 110: { atomicNumber: 110, symbol: \"Ds\", name: \"Darmstadtium\", mass: 281 },\n 111: { atomicNumber: 111, symbol: \"Rg\", name: \"Roentgenium\", mass: 282 },\n 112: { atomicNumber: 112, symbol: \"Cn\", name: \"Copernicium\", mass: 285 },\n 113: { atomicNumber: 113, symbol: \"Nh\", name: \"Nihonium\", mass: 286 },\n 114: { atomicNumber: 114, symbol: \"Fl\", name: \"Flerovium\", mass: 289 },\n 115: { atomicNumber: 115, symbol: \"Mc\", name: \"Moscovium\", mass: 289 },\n 116: { atomicNumber: 116, symbol: \"Lv\", name: \"Livermorium\", mass: 293 },\n 117: { atomicNumber: 117, symbol: \"Ts\", name: \"Tennessine\", mass: 294 },\n 118: { atomicNumber: 118, symbol: \"Og\", name: \"Oganesson\", mass: 294 },\n};\n\n/* Symbol-keyed element lookup, derived from PeriodicTable. /\nexport const elementBySymbol = Object.values(PeriodicTable).reduce(\n (acc, el) => {\n acc[el.symbol] = el;\n return acc;\n },\n {} as Record<string, ElementInfo>,\n);\n\n/* Look up an element by its chemical symbol.\n * @param symbol - Element symbol (e.g. \"Fe\")\n * @returns The matching ElementInfo, or undefined if not found. /\nexport function getElement(symbol: string): ElementInfo \| undefined {\n return elementBySymbol[symbol];\n}\n\n/\n Symbol → atomic number lookup (fast + safe)\n /\nexport const SymbolToAtomicNumber = new Map<string, number>(\n Object.values(PeriodicTable).map((el) => [el.symbol, el.atomicNumber]),\n);\n\n/* Atomic-number-to-symbol lookup map. /\nexport const AtomicNumberToSymbol = new Map<number, string>(\n Object.values(PeriodicTable).map((el) => [el.atomicNumber, el.symbol]),\n);\n","import { Structure } from \"../structure\";\nimport { Site } from \"../../site/site\";\nimport { getElement } from \"@/core/data/periodictable/atomicData\";\n\nfunction siteMass(site: Site): number {\n const siteMass = site.properties?.mass;\n\n if (typeof siteMass === \"number\") {\n return siteMass;\n }\n\n const speciesMass = site.species.properties?.mass;\n\n if (typeof speciesMass === \"number\") {\n return speciesMass;\n }\n\n const element = getElement(site.species.symbol);\n\n if (!element) {\n throw new Error(`Unknown element: ${site.species.symbol}`);\n }\n\n return element.mass;\n}\n\n/\n Sum the masses of all sites in the structure.\n * @param structure - Structure to evaluate.\n * @returns Total mass in atomic mass units.\n /\nexport function cellMass(structure: Structure): number {\n let mass = 0;\n\n for (const site of structure.sites) {\n mass += siteMass(site);\n }\n\n return mass;\n}\n","import { Structure } from \"../structure\";\nimport { volume } from \"./volume\";\nimport { cellMass } from \"./cellMass\";\n\n/\n Compute the density of a structure.\n * @param structure - Structure to evaluate.\n * @returns Density in amu/Ang^3.\n /\nexport function density(structure: Structure): number {\n const vol = volume(structure);\n\n if (vol < 1e-300) {\n throw new Error(\"Degenerate cell has no volume\");\n }\n\n return cellMass(structure) / vol;\n}\n","import { Structure } from \"../structure\";\nimport { Species } from \"../../species/species\";\n\n/\n Collect unique Species from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of unique Species.\n /\nexport function getSpecies(structure: Structure): Species[] {\n const species = new Map<string, Species>();\n\n for (const site of structure.sites) {\n const key = site.species.symbol;\n\n if (!species.has(key)) {\n species.set(key, site.species);\n }\n }\n\n return Array.from(species.values());\n}\n\n/\n Collect unique element symbols from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of element symbols.\n /\nexport function getElements(structure: Structure): string[] {\n return getSpecies(structure).map((s) => s.symbol);\n}\n\n/\n Count occurrences of each species symbol in a structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to occurrence counts.\n /\nexport function getSpeciesCounts(structure: Structure): Map<string, number> {\n const counts = new Map<string, number>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n counts.set(symbol, (counts.get(symbol) ?? 0) + 1);\n }\n\n return counts;\n}\n","import { Species } from \"../species/species\";\n\n/* Generic site properties map. /\nexport type SiteProperties = Record<string, any>;\n\n/* A 3D vector type. /\nexport type Vec3 = [number, number, number] \| Float64Array \| number[];\n\n/* A site with a species, fractional coordinates, and optional properties. /\nexport type Site<P extends SiteProperties = SiteProperties> = {\n species: Species;\n frac: Vec3;\n properties?: P;\n};\n\n/* Create a new Site object.\n * @param species - The species at the site.\n * @param frac - Fractional coordinates.\n * @param properties - Optional properties.\n * @returns A new Site. /\nexport function createSite<P extends SiteProperties>(\n species: Species,\n frac: Vec3,\n properties?: P,\n): Site<P> {\n return {\n species,\n frac,\n properties,\n };\n}\n","import { Lattice } from \"../lattice/lattice\";\nimport { Site } from \"./site\";\nimport { cartesian } from \"./cartesian\";\n\nimport { norm } from \"../matrix/operations/vector/norm\";\n\n/* Compute the minimum image distance between two sites.\n * @param lattice - The lattice.\n * @param a - First site.\n * @param b - Second site.\n * @returns Minimum image distance. /\nexport function distance(lattice: Lattice, a: Site, b: Site): number {\n const dFrac: [number, number, number] = [\n b.frac[0] - a.frac[0],\n b.frac[1] - a.frac[1],\n b.frac[2] - a.frac[2],\n ];\n\n for (let i = 0; i < 3; i++) {\n dFrac[i] -= Math.round(dFrac[i]);\n }\n\n const displaced: Site = {\n species: a.species,\n frac: dFrac,\n };\n\n const dCart = cartesian(lattice, displaced);\n\n return norm(dCart);\n}\n","import { Site, SiteProperties } from \"./site\";\n\nfunction wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n}\n\n/* Wrap a site's fractional coordinates into [0, 1).\n * @param site - The site to wrap.\n * @returns A new site with wrapped coordinates. /\nexport function wrap<T extends SiteProperties>(site: Site<T>): Site<T> {\n return {\n ...site,\n frac: [\n wrapValue(site.frac[0]),\n wrapValue(site.frac[1]),\n wrapValue(site.frac[2]),\n ],\n };\n}\n","/* A chemical species with a symbol and optional properties. /\nexport type Species<P extends Record<string, any> = Record<string, any>> = {\n symbol: string;\n properties?: P;\n};\n\n/* Create a new Species.\n * @param symbol - Element symbol.\n * @param properties - Optional properties.\n * @returns A new Species. /\nexport function createSpecies<P extends Record<string, any>>(\n symbol: string,\n properties?: P,\n): Species<P> {\n return { symbol, properties };\n}\n","export type {\n KPoints,\n KPath,\n KPoint,\n KPointSet,\n KGrid,\n Vec3,\n GridShape,\n} from \"./kpoints\";\n","import { Matrix } from \"../matrix\";\nimport { identity } from \"../matrix\";\n\n/* Scalar or multi-channel volumetric grid data. /\nexport interface VolumetricData {\n readonly data: Float64Array;\n readonly shape: [number, number, number];\n readonly channels: number;\n readonly basis?: Matrix;\n readonly origin: [number, number, number];\n readonly field?: string;\n readonly metadata?: Record<string, unknown>;\n}\n\ntype ReduceAxis = \"all\" \| \"channels\";\n\n/* Reduction axis configuration. /\nexport interface ReduceOptions {\n axis?: ReduceAxis;\n}\n\n/* Create a VolumetricData from shape and optional data buffer. /\nexport function createVolumetricData(params: {\n shape: [number, number, number];\n channels?: number;\n\n /\n Flat voxel-major buffer.\n \n Layout:\n * [v000c0, v000c1, ..., v001c0, v001c1, ...]\n /\n data?: Float64Array \| Iterable<number>;\n\n basis?: Matrix;\n origin?: [number, number, number];\n\n field?: string;\n metadata?: Record<string, unknown>;\n}): VolumetricData {\n const {\n shape,\n channels = 1,\n data,\n basis,\n origin = [0, 0, 0],\n field,\n metadata,\n } = params;\n\n const [D, H, W] = shape;\n const size = D H * W * channels;\n\n const buffer =\n data instanceof Float64Array\n ? data\n : data\n ? Float64Array.from(data)\n : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(\n `VolumetricData mismatch: expected ${size}, got ${buffer.length}`,\n );\n }\n\n return {\n data: buffer,\n shape,\n channels,\n basis: basis ?? identity(3),\n origin,\n field,\n metadata,\n };\n}\n\n/** Compute the flat buffer index for a voxel coordinate and channel. /\n/* * Performance-critical inner loops should generally use direct offset arithmetic.\n/** @param vol - Volumetric data. /\n/* @param x - Column index. /\n/* @param y - Row index. /\n/* @param z - Depth index. /\n/* @param c - Channel index. /\n/* @returns Linear index into the data buffer. /\nexport function index(\n vol: VolumetricData,\n x: number,\n y: number,\n z: number,\n c: number,\n) {\n const [D, H, W] = vol.shape;\n const { channels } = vol;\n\n return ((z H + y) * W + x) * channels + c;\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Create a volumetric grid filled with a constant value. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param value - Fill value. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData filled with value. /\nexport function fill(\n shape: [number, number, number],\n value: number,\n channels = 1,\n) {\n const size = shape[0] shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size).fill(value),\n });\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Generate volumetric data by evaluating a function over every voxel and channel. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param fn - Callback receiving (x, y, z, c) returning the value at that voxel. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData populated by fn. /\nexport function fromFunction(\n shape: [number, number, number],\n fn: (x: number, y: number, z: number, c: number) => number,\n channels = 1,\n) {\n const [D, H, W] = shape;\n const data = new Float64Array(D H * W * channels);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n for (let y = 0; y < H; y++) {\n for (let x = 0; x < W; x++) {\n for (let c = 0; c < channels; c++) {\n data[i++] = fn(x, y, z, c);\n }\n }\n }\n }\n\n return createVolumetricData({\n shape,\n channels,\n data,\n });\n}\n","import { Matrix } from \"../../matrix\";\nimport { createVolumetricData } from \"../volumetric\";\n\n/** Stack a list of 2-D Matrix slices into a 3-D volumetric grid. /\n/* @param slices - Array of matrices (depth dimension). /\n/* @returns A new VolumetricData with shape [slices.length, H, W]. /\nexport function fromMatrixSlices(slices: Matrix[]) {\n if (slices.length === 0) {\n throw new Error(\"No slices provided\");\n }\n\n const H = slices[0].rows;\n const W = slices[0].cols;\n const D = slices.length;\n\n const data = new Float64Array(D H * W);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n const m = slices[z];\n\n if (m.rows !== H \|\| m.cols !== W) {\n throw new Error(\"Inconsistent matrix slice dimensions\");\n }\n\n data.set(m.data, i);\n i += m.data.length;\n }\n\n return createVolumetricData({\n shape: [D, H, W],\n data,\n });\n}\n","import { fill } from \"./fill\";\n\n/** Create a volumetric grid filled with ones. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData with all values set to 1. /\nexport function ones(shape: [number, number, number], channels = 1) {\n return fill(shape, 1, channels);\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/* Create a volumetric grid filled with zeros. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData with all values set to 0. /\nexport function zeros(shape: [number, number, number], channels = 1) {\n const size = shape[0] shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size),\n });\n}\n","export interface SymmetryOperation {\n matrix: number[][];\n translation: number[];\n}\n\nfunction parseFraction(s: string): number {\n const trimmed = s.trim();\n\n if (trimmed.includes(\"/\")) {\n const [num, den] = trimmed.split(\"/\").map(Number);\n return num / den;\n }\n\n return Number(trimmed);\n}\n\nfunction parseComponent(expr: string): { coeffs: number[]; offset: number } {\n const cleaned = expr.replace(/\\s+/g, \"\");\n let offset = 0;\n const coeffs = [0, 0, 0];\n\n const terms = cleaned.match(/[+-]?[^+-]+/g) ?? [];\n\n const VAR_INDEX: Record<string, number> = { x: 0, y: 1, z: 2 };\n\n for (const term of terms) {\n const t = term.trim();\n\n if (t.length > 0 && VAR_INDEX[t.at(-1)!] !== undefined) {\n const idx = VAR_INDEX[t.at(-1)!];\n const sign = t.startsWith(\"-\") ? -1 : 1;\n\n coeffs[idx] += sign;\n } else {\n const frac = t.match(/([+-]?\\d+\\s\\/\\s\\d+)/);\n\n if (frac) {\n offset += parseFraction(frac[1].replace(/\\s/g, \"\"));\n } else {\n const val = Number(t);\n\n if (!isNaN(val)) {\n offset += val;\n }\n }\n }\n }\n\n return { coeffs, offset };\n}\n\n/** Parse a single symmetry operation string like '-y, x, z+1/2' into a matrix + translation.\n * @param op - The operation string (e.g. '-y, x, z+1/2').\n * @returns A SymmetryOperation with 3x3 matrix and translation vector. /\nexport function parseOperation(op: string): SymmetryOperation {\n const components = op.split(\",\").map((s) => parseComponent(s));\n\n return {\n matrix: components.map((c) => c.coeffs),\n translation: components.map((c) => c.offset),\n };\n}\n\n/* Parse all symmetry operation strings from a CIF _symmetry_equiv_pos_as_xyz loop.\n * @param ops - Array of operation strings (e.g. [\"x, y, z\", \"-x, -y, z\"]).\n * @returns Array of SymmetryOperation objects. /\nexport function parseOperations(ops: string[]): SymmetryOperation[] {\n return ops.map(parseOperation);\n}\n\n/* Apply a symmetry operation to fractional coordinates.\n * @param op - The symmetry operation.\n * @param frac - Fractional coordinates [x, y, z].\n * * @returns New fractional coordinates after applying the operation. /\nexport function applyOperation(\n op: SymmetryOperation,\n frac: number[],\n): number[] {\n const result = [0, 0, 0];\n\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n result[i] += op.matrix[i][j] frac[j];\n }\n\n result[i] += op.translation[i];\n }\n\n return result;\n}\n","/*\n Reads lines from a string one at a time, without pre-splitting into an array.\n /\nexport class LineReader {\n private pos = 0;\n /* Number of lines returned so far (including blank lines). /\n count = 0;\n\n constructor(private readonly text: string) {}\n\n /* Return the next line (without the newline character), or `null` at EOF. /\n next(): string \| null {\n if (this.pos >= this.text.length) return null;\n const end = this.text.indexOf(\"\\n\", this.pos);\n const line = end === -1 ? this.text.slice(this.pos) : this.text.slice(this.pos, end);\n this.pos = end === -1 ? this.text.length : end + 1;\n this.count++;\n return line;\n }\n\n /* Return a trimmed line, or throw on unexpected EOF. /\n nextTrimmed(): string {\n const line = this.next();\n if (line === null) throw new Error(\"Unexpected EOF\");\n return line.trim();\n }\n}\n","import { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { parameters } from \"../../lattice/parameters\";\nimport { Structure } from \"../../structure/structure\";\nimport {\n parseOperations,\n applyOperation,\n} from \"./symmetryOperations\";\nimport { LineReader } from \"../helpers\";\n\nfunction cleanValue(value: string \| undefined): number {\n if (value === undefined) return NaN;\n\n const unquoted = value.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n // remove uncertainty notation:\n // 5.432(1) -> 5.432\n return Number(unquoted.replace(/\$.+\$/, \"\"));\n}\n\nfunction tokenize(line: string): string[] {\n return line.match(/'[^']'\|\"[^\"]\"\|\\S+/g) ?? [];\n}\n\nfunction isSymOpHeader(header: string): boolean {\n const t = header.toLowerCase();\n return (\n t.includes(\"symmetry_equiv_pos\") \|\| t.includes(\"symop_operation_xyz\")\n );\n}\n\n/* Strips oxidation-state/charge suffixes (e.g. \"Na1+\" -> \"Na\", \"O2-\" -> \"O\"). /\nfunction cleanSpeciesSymbol(raw: string \| undefined): string {\n if (raw === undefined) return \"\";\n const unquoted = raw.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n const m = unquoted.match(/^([A-Z][a-z]?)/);\n return m ? m[1] : unquoted;\n}\n\n/* Parses a CIF (Crystallographic Information File) string into a Structure. /\nexport function fromCIF(text: string): Structure {\n let a = 0;\n let b = 0;\n let c = 0;\n\n let alpha = 0;\n let beta = 0;\n let gamma = 0;\n\n let atomHeaders: string[] = [];\n const atomRows: string[][] = [];\n\n let inLoop = false;\n let currentHeaders: string[] = [];\n let collectingAtoms = false;\n let collectingSymOps = false;\n // Headers mention atom sites but the loop kind is only known once data\n // starts (coordinate loop vs. aniso/geom/etc.). Resolved per loop.\n let potentialAtoms = false;\n let loopIsAniso = false;\n const symOpStrings: string[] = [];\n\n function resetLoopState() {\n inLoop = false;\n collectingAtoms = false;\n collectingSymOps = false;\n potentialAtoms = false;\n loopIsAniso = false;\n currentHeaders = [];\n }\n\n const r = new LineReader(text);\n let rawLine: string \| null;\n while ((rawLine = r.next()) !== null) {\n const line = rawLine.trim();\n if (!line) continue;\n\n // Comments and data/save blocks always terminate an active loop.\n if (line.startsWith(\"#\")) continue;\n if (line.startsWith(\"data_\") \|\| line.startsWith(\"save_\")) {\n resetLoopState();\n continue;\n }\n\n if (line === \"loop_\") {\n inLoop = true;\n currentHeaders = [];\n collectingAtoms = false;\n collectingSymOps = false;\n potentialAtoms = false;\n loopIsAniso = false;\n continue;\n }\n\n if (line.startsWith(\"_cell_length_a\")) {\n a = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_b\")) {\n b = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_c\")) {\n c = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_alpha\")) {\n alpha = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_beta\")) {\n beta = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_gamma\")) {\n gamma = cleanValue(tokenize(line)[1]);\n }\n\n if (inLoop && line.startsWith(\"_\")) {\n // A tag after data rows have started belongs outside the loop:\n // terminate the loop and treat it as a regular tag line.\n if (atomRows.length > 0 && collectingAtoms) {\n resetLoopState();\n continue;\n }\n if (symOpStrings.length > 0 && collectingSymOps) {\n resetLoopState();\n continue;\n }\n\n currentHeaders.push(line);\n\n if (isSymOpHeader(line)) {\n collectingSymOps = true;\n collectingAtoms = false;\n potentialAtoms = false;\n } else if (line.includes(\"_atom_site_aniso_\")) {\n // Anisotropic displacement parameters for the same sites —\n // never coordinate data.\n loopIsAniso = true;\n collectingAtoms = false;\n potentialAtoms = false;\n } else if (line.includes(\"_atom_site_\")) {\n // Could be the coordinate loop, but also matches geom loops\n // (e.g. `_geom_angle_atom_site_label_1`). Decided at data time.\n if (!loopIsAniso) potentialAtoms = true;\n collectingSymOps = false;\n }\n\n continue;\n }\n\n if (inLoop && potentialAtoms && !collectingAtoms) {\n // First data row of a candidate atom loop: only coordinate loops\n // (with fractional columns) are collected; aniso/geom/etc. ignored.\n const hasFract =\n currentHeaders.some((h) => h.includes(\"fract_x\")) \|\|\n currentHeaders.some((h) => h.includes(\"fract_y\")) \|\|\n currentHeaders.some((h) => h.includes(\"fract_z\"));\n\n if (!hasFract \|\| loopIsAniso) {\n potentialAtoms = false;\n } else {\n potentialAtoms = false;\n collectingAtoms = true;\n collectingSymOps = false;\n }\n }\n\n if (inLoop && collectingAtoms) {\n if (atomHeaders.length === 0) {\n atomHeaders = [...currentHeaders];\n }\n\n atomRows.push(tokenize(line));\n }\n\n if (inLoop && collectingSymOps) {\n // Symop rows look like `12 'x+1/2, y, -z'` or `x, y, z`.\n // Parse the whole line instead of individual tokens so unquoted\n // operations are not split apart.\n let s = line;\n const idMatch = s.match(/^\\d+\\s+(.)$/);\n if (idMatch) s = idMatch[1].trim();\n s = s.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n\n if (s.includes(\",\")) {\n symOpStrings.push(s);\n }\n }\n }\n\n const lattice = fromParameters(a, b, c, alpha, beta, gamma);\n\n const ix = atomHeaders.findIndex((x) => x.includes(\"fract_x\"));\n\n const iy = atomHeaders.findIndex((x) => x.includes(\"fract_y\"));\n\n const iz = atomHeaders.findIndex((x) => x.includes(\"fract_z\"));\n\n const ispecies = atomHeaders.findIndex((x) => x.includes(\"type_symbol\"));\n\n if (ix < 0 \|\| iy < 0 \|\| iz < 0 \|\| ispecies < 0) {\n throw new Error(\"Missing required atom site columns\");\n }\n\n const maxCol = Math.max(ix, iy, iz, ispecies);\n\n const asymSites = atomRows.map((row) => {\n if (row.length <= maxCol) {\n throw new Error(\"Incomplete atom site data row\");\n }\n\n return {\n species: {\n symbol: cleanSpeciesSymbol(row[ispecies]),\n },\n\n frac: new Float64Array([\n cleanValue(row[ix]),\n cleanValue(row[iy]),\n cleanValue(row[iz]),\n ]),\n };\n });\n\n if (symOpStrings.length === 0) {\n return { lattice, sites: asymSites };\n }\n\n const symOps = parseOperations(symOpStrings);\n\n const EPS = 1e-3;\n\n function wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n }\n\n function cleanNearZero(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n }\n\n function posKey(species: string, frac: number[]): string {\n const w = frac.map((v) => {\n const c = cleanNearZero(wrapValue(v));\n return Math.round(c * 1000) / 1000;\n });\n\n return `${species}:${w[0]},${w[1]},${w[2]}`;\n }\n\n const seen = new Set<string>();\n const sites: { species: { symbol: string }; frac: Float64Array }[] = [];\n\n for (const site of asymSites) {\n for (const op of symOps) {\n const operated = applyOperation(op, Array.from(site.frac));\n\n const frac = [\n cleanNearZero(wrapValue(operated[0])),\n cleanNearZero(wrapValue(operated[1])),\n cleanNearZero(wrapValue(operated[2])),\n ];\n\n const key = posKey(site.species.symbol, frac);\n\n if (!seen.has(key)) {\n seen.add(key);\n\n sites.push({\n species: { symbol: site.species.symbol },\n frac: new Float64Array(frac),\n });\n }\n }\n }\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a CIF string. /\nexport function toCIF(structure: Structure, precision = 6): string {\n const p = parameters(structure.lattice);\n\n const lines: string[] = [];\n\n lines.push(\"data_matsci-parse\");\n lines.push(\"\");\n\n lines.push(\"_symmetry_space_group_name_H-M 'P 1'\");\n lines.push(\"_symmetry_Int_Tables_number 1\");\n\n lines.push(\"\");\n\n lines.push(`_cell_length_a ${p[0].toFixed(precision)}`);\n\n lines.push(`_cell_length_b ${p[1].toFixed(precision)}`);\n\n lines.push(`_cell_length_c ${p[2].toFixed(precision)}`);\n\n lines.push(`_cell_angle_alpha ${p[3].toFixed(precision)}`);\n\n lines.push(`_cell_angle_beta ${p[4].toFixed(precision)}`);\n\n lines.push(`_cell_angle_gamma ${p[5].toFixed(precision)}`);\n\n lines.push(\"\");\n\n lines.push(\"loop_\");\n lines.push(\"_atom_site_label\");\n lines.push(\"_atom_site_type_symbol\");\n lines.push(\"_atom_site_fract_x\");\n lines.push(\"_atom_site_fract_y\");\n lines.push(\"_atom_site_fract_z\");\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n lines.push(\n `${site.species.symbol}${i + 1} ` +\n `${site.species.symbol} ` +\n `${site.frac[0].toFixed(precision)} ` +\n `${site.frac[1].toFixed(precision)} ` +\n `${site.frac[2].toFixed(precision)}`,\n );\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { cartesian, fractional } from \"../site\";\nimport { LineReader } from \"./helpers\";\n\nfunction isSelective(line: string): boolean {\n return line.toLowerCase().startsWith(\"selective\");\n}\n\nfunction isCartesian(line: string): boolean {\n const l = line.trim().toLowerCase();\n return l.startsWith(\"c\") \|\| l.startsWith(\"k\");\n}\n\n/* Parses a POSCAR/CONTCAR string into a Structure. /\nexport function fromPOSCAR(text: string): Structure {\n const r = new LineReader(text);\n\n // comment/title\n r.next();\n\n // scale factor\n const scale = Number(r.nextTrimmed());\n\n // lattice vectors (row-major)\n const latticeData: number[] = [];\n\n for (let i = 0; i < 3; i++) {\n const v = r.nextTrimmed().split(/\\s+/).map(Number);\n\n if (v.length !== 3) {\n throw new Error(\"Invalid POSCAR lattice\");\n }\n\n latticeData.push(v[0] scale, v[1] * scale, v[2] * scale);\n }\n\n const lattice = createLattice(latticeData);\n\n // VASP5 species names\n const symbols = r.nextTrimmed().split(/\\s+/);\n\n // atom counts\n const counts = r.nextTrimmed().split(/\\s+/).map(Number);\n\n if (symbols.length !== counts.length) {\n throw new Error(\"Species/count mismatch\");\n }\n\n // optional selective dynamics\n let selective = false;\n\n let line = r.nextTrimmed();\n if (isSelective(line)) {\n selective = true;\n line = r.nextTrimmed();\n }\n\n // direct is true unless cartesian is.\n let direct = true;\n direct = !isCartesian(line);\n\n const sites: Site[] = [];\n\n let speciesIndex = 0;\n let remaining = counts[0];\n\n const totalAtoms = counts.reduce((a, b) => a + b, 0);\n\n for (let i = 0; i < totalAtoms; i++) {\n const tokens = r.nextTrimmed().split(/\\s+/);\n\n const coords = tokens.slice(0, 3).map(Number);\n\n const frac = direct\n ? new Float64Array(coords)\n : fractional(lattice, new Float64Array(coords));\n\n const props: Record<string, unknown> = {};\n\n if (selective) {\n const sd = tokens.slice(3, 6).map((t) => t.toLowerCase() === \"t\");\n\n if (sd.length === 3) {\n props.selectiveDynamics = sd as [boolean, boolean, boolean];\n }\n }\n\n sites.push({\n species: {\n symbol: symbols[speciesIndex],\n },\n frac,\n ...(Object.keys(props).length > 0 ? { properties: props } : {}),\n });\n\n remaining--;\n\n if (remaining === 0 && speciesIndex < counts.length - 1) {\n speciesIndex++;\n remaining = counts[speciesIndex];\n }\n }\n\n return {\n lattice,\n sites,\n selectiveDynamics: selective \|\| undefined,\n _cursorEnd: r.count,\n };\n}\n\n/** Serializes a Structure to a POSCAR string. /\nexport function toPOSCAR(\n structure: Structure,\n options?: {\n title?: string;\n scale?: number;\n direct?: boolean;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n const scale = options?.scale ?? 1.0;\n const direct = options?.direct ?? true;\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(scale));\n\n // lattice\n const m = structure.lattice.basis.data;\n\n lines.push(`${m[0]} ${m[1]} ${m[2]}`);\n lines.push(`${m[3]} ${m[4]} ${m[5]}`);\n lines.push(`${m[6]} ${m[7]} ${m[8]}`);\n\n // preserve order of first appearance\n const grouped = new Map<string, typeof structure.sites>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n const group = grouped.get(symbol);\n\n if (group) {\n group.push(site);\n } else {\n grouped.set(symbol, [site]);\n }\n }\n\n\n const species = [...grouped.keys()];\n const sites = [...grouped.values()].flat();\n\n lines.push(species.join(\" \"));\n lines.push(species.map((s) => (grouped.get(s) ?? []).length).join(\" \"));\n\n const hasSelective = structure.selectiveDynamics ?? sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n lines.push(\"Selective Dynamics\");\n }\n\n lines.push(direct ? \"Direct\" : \"Cartesian\");\n\n for (const site of sites) {\n const coords = direct ? site.frac : cartesian(structure.lattice, site);\n\n let line = `${coords[0]} ${coords[1]} ${coords[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\n/* AiiDA-compatible site representation. /\nexport interface AiiDASite {\n position: [number, number, number];\n kind_name: string[];\n}\n\n/* AiiDA-compatible structure data format. /\nexport interface StructureData {\n cell: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ];\n kinds: [];\n sites: AiiDASite[];\n}\n\n/* Parses an AiiDA StructureData object into a Structure. /\nexport function fromStructureData(data: StructureData): Structure {\n const lattice = createLattice([\n ...data.cell[0],\n ...data.cell[1],\n ...data.cell[2],\n ]);\n\n const kindMap = new Map(data.kinds.map((kind: any) => [kind.name, kind]));\n\n const sites = data.sites.map((site: any) => {\n const kind = kindMap.get(site.kind_name);\n\n if (!kind) {\n throw new Error(`Unknown kind \"${site.kind_name}\"`);\n }\n\n return {\n species: {\n symbol: kind.symbols[0],\n },\n\n frac: fractional(lattice, new Float64Array(site.position)),\n };\n });\n\n return {\n lattice,\n sites,\n };\n}\n\n/* Serializes a Structure to an AiiDA StructureData-compatible object. /\nexport function toStructureData(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const symbols = [...new Set(structure.sites.map((s) => s.species.symbol))];\n\n const kinds = symbols.map((symbol) => ({\n name: symbol,\n symbols: [symbol],\n }));\n\n return {\n cell: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n kinds,\n\n sites: structure.sites.map((site) => ({\n kind_name: site.species.symbol,\n\n position: Array.from(cartesian(structure.lattice, site)),\n })),\n\n pbc1: true,\n pbc2: true,\n pbc3: true,\n };\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site/cartesian\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\nfunction nextSectionLine(r: LineReader, section: string): void {\n let line: string \| null;\n while ((line = r.next()) !== null) {\n if (line.trim().toUpperCase() === section) return;\n }\n throw new Error(`Missing ${section}`);\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\n/* Parses an XSF (XCrySDen Structure Format) string into a Structure. /\nexport function fromXSF(text: string): Structure {\n const r = new LineReader(text);\n\n nextSectionLine(r, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ]);\n\n nextSectionLine(r, \"PRIMCOORD\");\n\n const countLine = r.nextTrimmed();\n const [nAtoms] = countLine.split(/\\s+/).map(Number);\n\n if (!Number.isInteger(nAtoms) \|\| nAtoms < 0) {\n throw new Error(\"Invalid atom count in PRIMCOORD\");\n }\n\n const invData = inverse(lattice).data;\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = r.nextTrimmed().split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n sites.push({\n species: { symbol },\n // inlined frac conv for perf.\n frac: new Float64Array([\n invData[0] x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\n/** Serializes a Structure to an XSF string. /\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n lines.push(`${site.species.symbol} ${c[0]} ${c[1]} ${c[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice, Lattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\ntype PropDef = {\n name: string;\n type: string;\n count: number;\n offset: number;\n};\n\nfunction parseHeader(comment: string): ExtendedXYZInfo {\n const info: ExtendedXYZInfo = {};\n const kvRegex = /(\\w+)=(\".?\"\|\\S+)/g;\n\n for (const match of comment.matchAll(kvRegex)) {\n let value = match[2];\n if (value.startsWith('\"')) value = value.slice(1, -1);\n info[match[1]] = value;\n }\n\n return info;\n}\n\nfunction parseLattice(info: ExtendedXYZInfo) {\n if (!info.Lattice) {\n throw new Error(\"Extended XYZ must contain Lattice\");\n }\n\n const v = info.Lattice.split(/\\s+/).map(Number);\n if (v.length !== 9) throw new Error(\"Invalid Lattice\");\n\n return createLattice([v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]]);\n}\n\nfunction parseProperties(propStr: string): PropDef[] {\n const parts = propStr.split(\":\");\n const props: PropDef[] = [];\n let offset = 0;\n\n for (let i = 0; i < parts.length; i += 3) {\n const count = Number(parts[i + 2]);\n props.push({\n name: parts[i],\n type: parts[i + 1],\n count,\n offset,\n });\n offset += count;\n }\n\n return props;\n}\n\n/** Parses an extended XYZ string into a Structure. /\nexport function fromXYZ(text: string): Structure {\n const r = new LineReader(text);\n\n // skip leading blank lines\n let line: string \| null;\n do {\n line = r.next();\n } while (line !== null && line.trim().length === 0);\n\n if (line === null) throw new Error(\"XYZ file is too short\");\n\n const n = Number(line.trim());\n\n if (!Number.isInteger(n) \|\| n < 0) {\n throw new Error(\"Invalid atom count in XYZ file\");\n }\n\n const comment = r.next();\n if (comment === null) throw new Error(\"XYZ file is too short\");\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const propDefs = info.Properties\n ? parseProperties(info.Properties)\n : [\n { name: \"species\", type: \"S\", count: 1, offset: 0 },\n { name: \"pos\", type: \"R\", count: 3, offset: 1 },\n ];\n\n const sites: Site[] = [];\n\n let hasSelective = false;\n\n const invData = inverse(lattice).data;\n\n for (let i = 0; i < n; i++) {\n const atomLine = r.next();\n if (atomLine === null)\n throw new Error(\"Atom count exceeds available lines in XYZ file\");\n\n const tokens = atomLine.trim().split(/\\s+/);\n\n let symbol = \"\";\n let x = 0,\n y = 0,\n z = 0;\n const props: Record<string, unknown> = {};\n\n for (const def of propDefs) {\n const values = tokens.slice(def.offset, def.offset + def.count);\n\n if (def.name === \"species\") {\n symbol = values[0];\n } else if (def.name === \"pos\") {\n x = Number(values[0]);\n y = Number(values[1]);\n z = Number(values[2]);\n } else if (def.name === \"selectiveDynamics\") {\n const sd = values.map((v: string) => v.toLowerCase() === \"t\") as [\n boolean,\n boolean,\n boolean,\n ];\n props.selectiveDynamics = sd;\n hasSelective = true;\n } else {\n if (def.type === \"L\") {\n props[def.name] = values.map((v: string) => v.toLowerCase() === \"t\");\n } else if (def.type === \"R\" \|\| def.type === \"I\") {\n props[def.name] = values.map(Number);\n } else {\n props[def.name] = values.length === 1 ? values[0] : values;\n }\n }\n }\n\n if (!symbol) throw new Error(\"Missing species in XYZ\");\n if (!z && z !== 0) throw new Error(\"Invalid coordinates in XYZ\");\n\n const site: Site = {\n species: { symbol },\n // inlined site conv for perf.\n frac: new Float64Array([\n invData[0] x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n };\n\n if (Object.keys(props).length > 0) {\n site.properties = props;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n selectiveDynamics: hasSelective \|\| undefined,\n };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\n/** Serializes a Structure to an extended XYZ string. /\nexport function toXYZ(structure: Structure): string {\n const lines: string[] = [];\n\n const sites = structure.sites;\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n const propParts: string[] = [\"species\", \"S\", \"1\", \"pos\", \"R\", \"3\"];\n const hasSelective =\n structure.selectiveDynamics ??\n sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n propParts.push(\"selectiveDynamics\", \"L\", \"3\");\n }\n\n lines.push(`Lattice=\"${latticeStr}\" Properties=${propParts.join(\":\")}`);\n\n for (const site of sites) {\n const cart = cartesian(structure.lattice, site);\n let line = `${site.species.symbol} ${cart[0]} ${cart[1]} ${cart[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice\";\n\nimport { fractional, cartesian } from \"../site\";\nimport { Structure } from \"../structure\";\n\n/* Parses an OPTIMADE structure data object into a Structure. /\nexport function fromOptimade(data: any): Structure {\n const lattice = createLattice([\n ...data.attributes.lattice_vectors[0],\n ...data.attributes.lattice_vectors[1],\n ...data.attributes.lattice_vectors[2],\n ]);\n\n const positions = data.attributes.cartesian_site_positions;\n const species = data.attributes.species_at_sites;\n\n const sites = positions.map((position: number[], i: number) => ({\n species: {\n symbol: species[i],\n },\n\n frac: fractional(lattice, new Float64Array(position)),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\n/* Serializes a Structure to an OPTIMADE-compatible data object. /\nexport function toOptimade(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const species_at_sites = structure.sites.map((site) => site.species.symbol);\n\n const elements = [...new Set(species_at_sites)].sort();\n\n return {\n attributes: {\n lattice_vectors: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n species_at_sites,\n\n cartesian_site_positions: structure.sites.map((site) =>\n Array.from(cartesian(structure.lattice, site)),\n ),\n\n dimension_types: [1, 1, 1],\n\n nsites: structure.sites.length,\n\n nelements: elements.length,\n\n elements,\n },\n };\n}\n","/\n Convert a single measurement between units.\n \n Note on floating point: conversion routes through the base unit, so each\n * call applies two roundings (`value * fromFactor / toFactor`). The result\n * can differ by 1 ulp from multiplying by a direct factor (e.g.\n * `convert(v, \"Hartree\", \"Rydberg\")` is not bit-identical to `v * 2` for all\n * doubles). Callers that need bit-exact round-trips should resolve the\n * factor once (e.g. `convert(1, from, to)`) and apply it in a tight loop\n * instead of converting per value — which is also much faster.\n \n @param value - Numeric value to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Converted value.\n /\nexport function convertMeasurement<T extends string>(\n value: number,\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number {\n const resolve = (u: string) => (aliases?.[u] ?? u) as T;\n\n const fromUnit = resolve(from);\n const toUnit = resolve(to);\n\n if (fromUnit === toUnit) return value;\n\n const valueInBase = value conversions[fromUnit];\n return valueInBase / conversions[toUnit];\n}\n\n/*\n Convert an array of measurements between units.\n \n Same floating-point caveat as convertMeasurement applies per element; in\n * addition this allocates a plain number[] and performs map lookups per\n * value, so for large typed arrays prefer resolving the factor once and\n * looping directly.\n \n @param arr - Array of numeric values to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Array of converted values.\n /\nexport function convertMeasurementArray<T extends string>(\n arr: number[],\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number[] {\n return arr.map((v) => convertMeasurement(v, from, to, conversions, aliases));\n}\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported length unit identifiers. /\nexport type LengthUnits =\n \| \"angstrom\"\n \| \"bohr\"\n \| \"nm\"\n \| \"pm\"\n \| \"cm\"\n \| \"m\"\n \| \"um\"\n \| \"fm\";\n\nconst LengthConversions: Record<LengthUnits, number> = {\n angstrom: 1,\n bohr: 0.529177,\n nm: 10,\n pm: 0.01,\n um: 1e4,\n cm: 1e8,\n m: 1e10,\n fm: 1e-5,\n};\n\nconst LengthAliases: Record<string, LengthUnits> = {\n Å: \"angstrom\",\n μm: \"um\",\n};\n\n/* Unit system for length conversions with angstrom as base. /\nexport const LengthUnitSystem = {\n conversions: LengthConversions,\n aliases: LengthAliases,\n\n convert(value: number, from: LengthUnits \| string, to: LengthUnits \| string) {\n return convertMeasurement(\n value,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: LengthUnits \| string,\n to: LengthUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n};\n","// derived from https://manual.gromacs.org/current/reference-manual/file-formats.html#gro\n\n// NOTE: GROMACS stores all lengths (coordinates and box vectors) in nm.\n// Internally matsci-parse uses Å.\n\n// Its common convention for GROMACs to use Hw or Ow for water, we dont try to fix this at-all\n// therefore cross format parsing (to a software that needs elemental indication) will probably fail.\n\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LengthUnitSystem } from \"../units/length\";\n\nfunction pad5(str: string) {\n return str.length > 5 ? str.slice(0, 5) : str.padStart(5);\n}\n\nfunction formatCoord(x: number) {\n return x.toFixed(3).padStart(8);\n}\n\n/* Parses a GROMACS GRO string into a Structure. /\nexport function fromGRO(text: string): Structure {\n const lines = text.split(/\\r?\\n/).filter((l) => l.length > 0);\n\n let cursor = 0;\n\n const title = lines[cursor++];\n\n const timeMatch = title.match(/t=\\s([-+]?[0-9]\\.?[0-9]+)/i);\n const time = timeMatch ? Number(timeMatch[1]) : undefined;\n\n const nAtoms = Number(lines[cursor++]);\n\n if (!Number.isFinite(nAtoms)) {\n throw new Error(\"Invalid GRO atom count\");\n }\n\n type Atom = {\n symbol: string;\n cart: Float64Array;\n };\n\n const atoms: Atom[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const line = lines[cursor++];\n\n const x = Number(line.slice(20, 28));\n const y = Number(line.slice(28, 36));\n const z = Number(line.slice(36, 44));\n\n let atomName = line.slice(10, 15).trim();\n\n let symbol = atomName.replace(/[0-9]/g, \"\");\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n\n atoms.push({\n symbol,\n cart: new Float64Array(\n LengthUnitSystem.convertArray([x, y, z], \"nm\", \"angstrom\"),\n ),\n });\n }\n\n let lattice = null;\n\n const boxLine = lines[cursor];\n\n if (boxLine) {\n const vals = boxLine.trim().split(/\\s+/).map(Number);\n\n const matrix = LengthUnitSystem.convertArray(\n [\n vals[0] ?? 0,\n vals[3] ?? 0,\n vals[4] ?? 0,\n vals[5] ?? 0,\n vals[1] ?? 0,\n vals[6] ?? 0,\n vals[7] ?? 0,\n vals[8] ?? 0,\n vals[2] ?? 0,\n ],\n \"nm\",\n \"angstrom\",\n );\n\n const hasOffDiagonal =\n matrix[1] !== 0 \|\|\n matrix[2] !== 0 \|\|\n matrix[3] !== 0 \|\|\n matrix[5] !== 0 \|\|\n matrix[6] !== 0 \|\|\n matrix[7] !== 0;\n\n lattice = hasOffDiagonal\n ? createLattice(matrix)\n : createLattice([matrix[0], matrix[4], matrix[8]]);\n }\n\n const sites: Site[] = atoms.map((atom) => ({\n species: { symbol: atom.symbol },\n frac: lattice\n ? fractional(lattice, atom.cart)\n : new Float64Array([NaN, NaN, NaN]),\n }));\n\n return {\n lattice,\n sites,\n time,\n };\n}\n\n/* Serializes a Structure to a GROMACS GRO string. /\nexport function toGRO(\n structure: Structure,\n options?: {\n title?: string;\n time?: number;\n },\n): string {\n const title =\n options?.title ??\n (options?.time !== undefined\n ? `Generated structure, t=${options.time}`\n : \"Generated by matsci-parse\");\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(structure.sites.length));\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n\n const [x, y, z] = LengthUnitSystem.convertArray(\n Array.from(cart),\n \"angstrom\",\n \"nm\",\n );\n\n lines.push(\n pad5(\"1\") +\n pad5(\"RES\") +\n pad5(site.species.symbol) +\n pad5(String(i + 1)) +\n formatCoord(x) +\n formatCoord(y) +\n formatCoord(z),\n );\n }\n\n const m = structure.lattice.basis.data;\n\n const [a, b, c] = LengthUnitSystem.convertArray(\n [m[0], m[4], m[8]],\n \"angstrom\",\n \"nm\",\n );\n\n lines.push([a, b, c].map((v) => v.toFixed(5)).join(\" \"));\n\n return lines.join(\"\\n\");\n}\n","import { fromParameters } from \"../lattice\";\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nconst DEFAULT_PADDING = 10.0;\n\nfunction parseCRYST1(line: string) {\n const a = Number(line.slice(6, 15));\n const b = Number(line.slice(15, 24));\n const c = Number(line.slice(24, 33));\n\n const alpha = Number(line.slice(33, 40));\n const beta = Number(line.slice(40, 47));\n const gamma = Number(line.slice(47, 54));\n\n return { a, b, c, alpha, beta, gamma };\n}\n\nfunction isCRYST1Sane(\n a: number,\n b: number,\n c: number,\n extentX: number,\n extentY: number,\n extentZ: number,\n): boolean {\n // reject degenerate or identity cells\n if (a <= 1e-3 \|\| b <= 1e-3 \|\| c <= 1e-3) return false;\n\n // reject clearly too small cells\n const margin = 1.2; // allow small packing inefficiency\n\n if (a < extentX margin) return false;\n if (b < extentY * margin) return false;\n if (c < extentZ * margin) return false;\n\n // also reject ridiculous huge identity placeholders\n if (a === 1 && b === 1 && c === 1) return false;\n\n return true;\n}\n\n/** Parses a PDB (Protein Data Bank) string into a Structure. /\nexport function fromPDB(text: string): Structure {\n const lines = text.split(/\\r?\\n/);\n\n let crystal: {\n a: number;\n b: number;\n c: number;\n alpha: number;\n beta: number;\n gamma: number;\n } \| null = null;\n\n type ParsedAtom = {\n symbol: string;\n x: number;\n y: number;\n z: number;\n };\n\n const atoms: ParsedAtom[] = [];\n\n let xmin = Infinity;\n let ymin = Infinity;\n let zmin = Infinity;\n\n let xmax = -Infinity;\n let ymax = -Infinity;\n let zmax = -Infinity;\n\n for (const line of lines) {\n if (line.startsWith(\"CRYST1\")) {\n crystal = parseCRYST1(line);\n continue;\n }\n\n if (!line.startsWith(\"ATOM \") && !line.startsWith(\"HETATM\")) {\n continue;\n }\n\n const x = Number(line.slice(30, 38));\n const y = Number(line.slice(38, 46));\n const z = Number(line.slice(46, 54));\n\n let symbol = line.slice(76, 78).trim();\n\n if (!symbol) {\n symbol = line.slice(12, 16).replace(/[0-9]/g, \"\").trim();\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n }\n\n atoms.push({ symbol, x, y, z });\n\n xmin = Math.min(xmin, x);\n ymin = Math.min(ymin, y);\n zmin = Math.min(zmin, z);\n\n xmax = Math.max(xmax, x);\n ymax = Math.max(ymax, y);\n zmax = Math.max(zmax, z);\n }\n\n if (atoms.length === 0) {\n throw new Error(\"No ATOM/HETATM records found.\");\n }\n\n const extentX = xmax - xmin;\n const extentY = ymax - ymin;\n const extentZ = zmax - zmin;\n\n let lattice = createLattice([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n\n let originX = xmin - DEFAULT_PADDING;\n let originY = ymin - DEFAULT_PADDING;\n let originZ = zmin - DEFAULT_PADDING;\n\n const useCrystal =\n crystal !== null &&\n isCRYST1Sane(crystal.a, crystal.b, crystal.c, extentX, extentY, extentZ);\n\n if (useCrystal) {\n lattice = fromParameters(\n crystal.a,\n crystal.b,\n crystal.c,\n crystal.alpha,\n crystal.beta,\n crystal.gamma,\n );\n\n originX = 0;\n originY = 0;\n originZ = 0;\n } else {\n const a = Math.max(extentX + 2 DEFAULT_PADDING, 1.0);\n const b = Math.max(extentY + 2 * DEFAULT_PADDING, 1.0);\n const c = Math.max(extentZ + 2 * DEFAULT_PADDING, 1.0);\n\n lattice = createLattice([a, 0, 0, 0, b, 0, 0, 0, c]);\n }\n\n const sites: Site[] = atoms.map(({ symbol, x, y, z }) => ({\n species: { symbol },\n frac: fractional(\n lattice,\n new Float64Array([x - originX, y - originY, z - originZ]),\n ),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a PDB string. /\nexport function toPDB(\n structure: Structure,\n options?: {\n title?: string;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n\n const lines: string[] = [];\n\n lines.push(`HEADER ${title}`);\n\n let index = 1;\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n const symbol = site.species.symbol;\n\n lines.push(\n [\n \"ATOM \",\n index.toString().padStart(5),\n \" \",\n symbol.padEnd(4),\n \" MOL \",\n \"A\",\n \" 1 \",\n c[0].toFixed(3).padStart(8),\n c[1].toFixed(3).padStart(8),\n c[2].toFixed(3).padStart(8),\n \" 1.00\",\n \" 0.00\",\n \" \",\n symbol.padStart(2),\n ].join(\"\"),\n );\n\n index++;\n }\n\n lines.push(\"END\");\n\n return lines.join(\"\\n\");\n}\n","/\n QE ibrav → Lattice vector mapping.\n \n Implements all 29 QE ibrav values (-14 to +14, excluding 0).\n * Maps the ibrav index + celldm or A,B,C parameters to a 3x3 lattice basis.\n \n @see https://www.quantum-espresso.org/Doc/INPUT_PW.html\n /\n\nimport { createLattice } from \"../../lattice\";\nimport type { Lattice } from \"../../lattice\";\nimport { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { clean } from \"../../math/numeric\";\n\nconst SQRT3 = Math.sqrt(3);\nconst SQRT2 = Math.sqrt(2);\n\n/\n Construct a Lattice from QE ibrav index and crystal parameters.\n \n Output units: Bohr. The caller must convert to Angstrom if needed.\n \n @param ibrav Bravais lattice index (-14 to +14, excluding 0)\n * @param celldm celldm(1..6): celldm(1) in Bohr, others unitless ratios/cosines\n * @param ABC Optional alternative: [A, B, C, cosAB, cosAC, cosBC] with A,B,C in Angstrom\n /\nexport function ibravToLattice(\n ibrav: number,\n celldm: number[],\n ABC?: [number, number, number, number, number, number],\n): Lattice {\n if (ibrav === 0) {\n throw new Error(\"ibrav=0 requires explicit CELL_PARAMETERS\");\n }\n\n // resolve lattice parameter a in Bohr\n let a: number;\n let b: number;\n let c: number;\n let cosab: number;\n let cosac: number;\n let cosbc: number;\n\n if (ABC) {\n // A,B,C in Angstrom → convert to Bohr\n const [Av, Bv, Cv, cosAB, cosAC, cosBC] = ABC;\n a = Av BOHR_PER_ANGSTROM;\n b = Bv * BOHR_PER_ANGSTROM;\n c = Cv * BOHR_PER_ANGSTROM;\n cosab = cosAB;\n cosac = cosAC;\n cosbc = cosBC;\n } else {\n a = celldm[0] ?? 0;\n b = a * (celldm[1] ?? 0);\n c = a * (celldm[2] ?? 0);\n\n // meaning of celldm(4..6) depends on ibrav\n // defaults set per-case below\n cosab = 0;\n cosac = 0;\n cosbc = 0;\n }\n\n const v: number[] = new Array(9);\n\n switch (ibrav) {\n case 1: {\n // Cubic P (sc): v1 = a(1,0,0), v2 = a(0,1,0), v3 = a(0,0,1)\n const pp = fromParameters(a, a, a, 90, 90, 90);\n return pp;\n }\n\n case 2: {\n // Cubic F (fcc): v1 = (a/2)(-1,0,1), v2 = (a/2)(0,1,1), v3 = (a/2)(-1,1,0)\n const h = a / 2;\n v[0] = -h; v[1] = 0; v[2] = h;\n v[3] = 0; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = h; v[8] = 0;\n break;\n }\n\n case 3: {\n // Cubic I (bcc): v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1)\n const h = a / 2;\n v[0] = h; v[1] = h; v[2] = h;\n v[3] = -h; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = -h; v[8] = h;\n break;\n }\n\n case -3: {\n // Cubic I (bcc), more symmetric: v1 = (a/2)(-1,1,1), v2 = (a/2)(1,-1,1), v3 = (a/2)(1,1,-1)\n const h = a / 2;\n v[0] = -h; v[1] = h; v[2] = h;\n v[3] = h; v[4] = -h; v[5] = h;\n v[6] = h; v[7] = h; v[8] = -h;\n break;\n }\n\n case 4: {\n // Hexagonal and Trigonal P: celldm(3) = c/a\n // v1 = a(1,0,0), v2 = a(-1/2, sqrt(3)/2, 0), v3 = a(0,0,c/a)\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 120);\n }\n\n case 5: {\n // Trigonal R, 3fold axis c: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n v[0] = a * tx; v[1] = -a * ty; v[2] = a * tz;\n v[3] = 0; v[4] = a * 2 * ty; v[5] = a * tz;\n v[6] = -a * tx; v[7] = -a * ty; v[8] = a * tz;\n break;\n }\n\n case -5: {\n // Trigonal R, 3fold axis <111>: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n const u = tz - 2 * SQRT2 * ty;\n const vv = tz + SQRT2 * ty;\n const ap = a / SQRT3;\n v[0] = ap * u; v[1] = ap * vv; v[2] = ap * vv;\n v[3] = ap * vv; v[4] = ap * u; v[5] = ap * vv;\n v[6] = ap * vv; v[7] = ap * vv; v[8] = ap * u;\n break;\n }\n\n case 6: {\n // Tetragonal P (st): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 90);\n }\n\n case 7: {\n // Tetragonal I (bct): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const h = a / 2;\n const hh = h * ca;\n v[0] = h; v[1] = -h; v[2] = hh;\n v[3] = h; v[4] = h; v[5] = hh;\n v[6] = -h; v[7] = -h; v[8] = hh;\n break;\n }\n\n case 8: {\n // Orthorhombic P: celldm(2) = b/a, celldm(3) = c/a\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a * ba, a * ca, 90, 90, 90);\n }\n\n case 9: {\n // Orthorhombic base-centered (bco): celldm(2) = b/a, celldm(3) = c/a\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case -9: {\n // Orthorhombic BC, alternate: v1 = (a/2, -b/2, 0), v2 = (a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = -bb / 2; v[2] = 0;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case 91: {\n // Orthorhombic one-face base-centered A-type\n // v1 = (a, 0, 0), v2 = (0, b/2, -c/2), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a; v[1] = 0; v[2] = 0;\n v[3] = 0; v[4] = bb / 2; v[5] = -cc / 2;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 10: {\n // Orthorhombic face-centered\n // v1 = (a/2, 0, c/2), v2 = (a/2, b/2, 0), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = cc / 2;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 11: {\n // Orthorhombic body-centered\n // v1 = (a/2, b/2, c/2), v2 = (-a/2, b/2, c/2), v3 = (-a/2, -b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = cc / 2;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = cc / 2;\n v[6] = -a / 2; v[7] = -bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 12: {\n // Monoclinic P, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const gamma = Math.acos(cg) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, 90, gamma);\n }\n\n case -12: {\n // Monoclinic P, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const beta = Math.acos(cb) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, beta, 90);\n }\n\n case 13: {\n // Monoclinic base-centered, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n // v1 = (a/2, 0, -c/2), v2 = (bcos(gamma), bsin(gamma), 0), v3 = (a/2, 0, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const sg = Math.sqrt(Math.max(0, 1 - cg * cg));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = -cc / 2;\n v[3] = bb * cg; v[4] = bb * sg; v[5] = 0;\n v[6] = a / 2; v[7] = 0; v[8] = cc / 2;\n break;\n }\n\n case -13: {\n // Monoclinic base-centered, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (ccos(beta), 0, csin(beta))\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const sb = Math.sqrt(Math.max(0, 1 - cb * cb));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = cc * cb; v[7] = 0; v[8] = cc * sb;\n break;\n }\n\n case 14: {\n // Triclinic: celldm(2..6)\n // Same as fromParameters with explicit angles\n if (ABC) {\n return fromParameters(a, b, c,\n Math.acos(cosbc) * (180 / Math.PI),\n Math.acos(cosac) * (180 / Math.PI),\n Math.acos(cosab) * (180 / Math.PI),\n );\n }\n const ba = celldm[1] ?? 1;\n const ca = celldm[2] ?? 1;\n const cbc = celldm[3] ?? 0; // cos(alpha) between b and c\n const cac = celldm[4] ?? 0; // cos(beta) between a and c\n const cab = celldm[5] ?? 0; // cos(gamma) between a and b\n const bb = a * ba;\n const cc = a * ca;\n return fromParameters(a, bb, cc,\n Math.acos(cbc) * (180 / Math.PI),\n Math.acos(cac) * (180 / Math.PI),\n Math.acos(cab) * (180 / Math.PI),\n );\n }\n\n default:\n throw new Error(`Unsupported ibrav value: ${ibrav}`);\n }\n\n return createLattice(v.map(clean));\n}\n","/*\n Quantum ESPRESSO Fortran namelist parser.\n \n Parses QE-style namelists (`&NAME ... /`) from input text.\n * Supports strings, reals (including Fortran D notation),\n * logicals, integers, and array syntax `key(i) = value`.\n /\n\nexport interface QeNamelist {\n /* Namelist block name (uppercase). /\n name: string;\n /* Key → raw string value (keys stored lowercase). /\n values: Map<string, string>;\n}\n\nfunction convertFortranReal(s: string): string {\n const v = s.replace(/[dD]/g, \"e\");\n return String(Number.parseFloat(v));\n}\n\nfunction convertValue(raw: string): string {\n const trimmed = raw.trim();\n\n // quoted string\n if (\n (trimmed.startsWith(\"'\") && trimmed.endsWith(\"'\")) \|\|\n (trimmed.startsWith('\"') && trimmed.endsWith('\"'))\n ) {\n return trimmed.slice(1, -1);\n }\n\n // logical\n if (/^\\.(?:true\|false)\\.$/i.test(trimmed)) {\n return trimmed.toLowerCase() === \".true.\" ? \"true\" : \"false\";\n }\n\n // Fortran D-notation real\n if (/[dD]/.test(trimmed)) {\n return convertFortranReal(trimmed);\n }\n\n return trimmed;\n}\n\n/\n Parse a single QE namelist block from lines.\n * Returns the namelist and the index after the closing `/`.\n /\nfunction parseOne(\n lines: string[],\n start: number,\n): { namelist: QeNamelist; end: number } \| null {\n const openLine = lines[start].trim();\n\n const openMatch = openLine.match(/^&(\\w+)/i);\n if (!openMatch) return null;\n\n const name = openMatch[1].toUpperCase();\n const values = new Map<string, string>();\n\n for (let i = start + 1; i < lines.length; i++) {\n let line = lines[i];\n\n // strip inline comments\n const commentIdx = line.indexOf(\"!\");\n if (commentIdx >= 0) line = line.slice(0, commentIdx);\n\n // closing slash\n if (/^\\//.test(line.trim())) {\n return { namelist: { name, values }, end: i };\n }\n\n // key = value pairs (commas optional)\n const pairs = line.split(\",\");\n for (const pair of pairs) {\n const eqIdx = pair.indexOf(\"=\");\n if (eqIdx < 0) continue;\n\n const key = pair.slice(0, eqIdx).trim().toLowerCase();\n const raw = pair.slice(eqIdx + 1);\n\n if (!key) continue;\n\n // check for array syntax: key(i)\n const arrMatch = key.match(/^(\\w+)\$(\\d+)\$$/);\n const storeKey = arrMatch ? `${arrMatch[1]}(${arrMatch[2]})` : key;\n\n values.set(storeKey, convertValue(raw));\n }\n }\n\n // unterminated namelist\n return { namelist: { name, values }, end: lines.length };\n}\n\n/\n Parse all QE namelists from input text.\n * Returns namelists in order of appearance.\n /\nexport function parseQeNamelist(text: string): QeNamelist[] {\n const lines = text.split(\"\\n\");\n const result: QeNamelist[] = [];\n\n for (let i = 0; i < lines.length; i++) {\n if (/^\\s&\\w+/.test(lines[i])) {\n const parsed = parseOne(lines, i);\n if (parsed) {\n result.push(parsed.namelist);\n i = parsed.end;\n }\n }\n }\n\n return result;\n}\n\n/** Find a namelist block by name. /\nfunction findBlock(\n namelists: QeNamelist[],\n block: string,\n): QeNamelist \| undefined {\n const upper = block.toUpperCase();\n return namelists.find((n) => n.name === upper);\n}\n\n/* Get a raw string value from a namelist block. /\nexport function getString(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): string \| undefined {\n return findBlock(namelists, block)?.values.get(key.toLowerCase());\n}\n\n/* Get a numeric value from a namelist block. /\nexport function getNumber(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): number \| undefined {\n const raw = getString(namelists, block, key);\n if (raw === undefined) return undefined;\n const n = Number.parseFloat(raw);\n return Number.isNaN(n) ? undefined : n;\n}\n\n/* Get an array value (e.g. celldm(1)..celldm(6)) from a namelist block. /\nexport function getArray(\n namelists: QeNamelist[],\n block: string,\n key: string,\n size: number,\n): number[] {\n const lower = key.toLowerCase();\n const result: number[] = [];\n for (let i = 1; i <= size; i++) {\n const raw = getString(namelists, block, `${lower}(${i})`);\n if (raw !== undefined) {\n result.push(Number.parseFloat(raw));\n } else {\n result.push(0);\n }\n }\n return result;\n}\n","import { createLattice } from \"../../lattice/lattice\";\nimport { kspacingToGrid } from \"../../lattice/kspacingToGrid\";\nimport { ibravToLattice } from \"./ibrav\";\nimport { fractional } from \"../../site\";\nimport { getElement } from \"../../data/periodictable/atomicData\";\nimport type { Site } from \"../../site/site\";\nimport type { Structure } from \"../../structure/structure\";\nimport { parseQeNamelist, getNumber, getString, getArray } from \"./namelist\";\nimport type {\n AtomicSpeciesEntry,\n AtomicPositionEntry,\n CellParameterEntry,\n KPointsCard,\n} from \"./schema/cards\";\nimport type { QeControlOptions } from \"./schema/control\";\nimport type { QeSystemOptions } from \"./schema/system\";\nimport type { QeElectronsOptions } from \"./schema/electrons\";\n\nconst BOHR_TO_ANGSTROM = 0.529177;\n\ntype AtomCoordMode = \"crystal\" \| \"angstrom\" \| \"bohr\" \| \"alat\";\n\n// ──────────────────────────────────────────────────────────────────────\n// Options — composed from schema types\n// ──────────────────────────────────────────────────────────────────────\n\n/* User-facing options for {@link toPW}. Composed from schema types. /\nexport interface QEOptions {\n control?: QeControlOptions;\n system?: QeSystemOptions;\n electrons?: QeElectronsOptions;\n kpoints?:\n \| { grid: [number, number, number]; shift?: [number, number, number] }\n \| { kspacing: number };\n pseudo?: { pseudos?: Record<string, string> };\n}\n\nconst QE_DEFAULTS: Required<\n Pick<QEOptions, \"control\" \| \"system\" \| \"electrons\" \| \"kpoints\" \| \"pseudo\">\n> = {\n control: {\n title: \"Generated by matsci-parse\",\n calculation: \"scf\",\n pseudo_dir: \"./\",\n },\n system: {\n ecutwfc: 30,\n },\n electrons: {\n conv_thr: 1e-6,\n },\n kpoints: { kspacing: 0.22 },\n pseudo: { pseudos: {} },\n};\n\n// ──────────────────────────────────────────────────────────────────────\n// fromPW — unchanged\n// ──────────────────────────────────────────────────────────────────────\n\n/* Parses a Quantum ESPRESSO PW input string into a Structure. /\nexport function fromPW(text: string): Structure {\n const namelists = parseQeNamelist(text);\n const lines = text.split(\"\\n\");\n\n // --- extract &SYSTEM parameters ---\n const ibrav = getNumber(namelists, \"SYSTEM\", \"ibrav\") ?? 0;\n const nat = getNumber(namelists, \"SYSTEM\", \"nat\");\n const celldm = getArray(namelists, \"SYSTEM\", \"celldm\", 6);\n\n // --- build lattice ---\n let lattice: ReturnType<typeof createLattice>;\n\n if (ibrav !== 0) {\n // ibravToLattice returns lattice vectors in Bohr → convert to angstrom\n const bohr = ibravToLattice(ibrav, celldm);\n const m = bohr.basis.data;\n lattice = createLattice([\n m[0] BOHR_TO_ANGSTROM,\n m[1] * BOHR_TO_ANGSTROM,\n m[2] * BOHR_TO_ANGSTROM,\n m[3] * BOHR_TO_ANGSTROM,\n m[4] * BOHR_TO_ANGSTROM,\n m[5] * BOHR_TO_ANGSTROM,\n m[6] * BOHR_TO_ANGSTROM,\n m[7] * BOHR_TO_ANGSTROM,\n m[8] * BOHR_TO_ANGSTROM,\n ]);\n } else {\n // ibrav=0: lattice must come from CELL_PARAMETERS block\n const { lattice: cellLattice, units: cellUnits } =\n parseCellParameters(lines);\n\n if (cellUnits === \"alat\") {\n if (celldm[0] === 0) {\n throw new Error(\"CELL_PARAMETERS alat requires celldm(1) in &SYSTEM\");\n }\n // lattice vectors are in units of celldm(1) Bohr → convert to angstrom\n const factor = celldm[0] / BOHR_TO_ANGSTROM;\n const m = cellLattice.basis.data;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else if (cellUnits === \"bohr\") {\n // lattice vectors in Bohr → convert to angstrom\n const m = cellLattice.basis.data;\n const factor = 1 / BOHR_TO_ANGSTROM;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else {\n // angstrom — use directly\n lattice = cellLattice;\n }\n }\n\n // --- parse atomic positions ---\n const {\n lines: atomLines,\n units,\n selectiveDynamics,\n } = parseAtomicPositions(lines);\n\n if (atomLines.length === 0) {\n throw new Error(\"ATOMIC_POSITIONS block not found\");\n }\n\n if (nat !== undefined && atomLines.length !== nat) {\n throw new Error(\n `Expected ${nat} atoms (from &SYSTEM nat), got ${atomLines.length}`,\n );\n }\n\n const sites: Site[] = [];\n\n for (const line of atomLines) {\n const parts = line.split(/\\s+/);\n const symbol = parts[0];\n const x = +parts[1];\n const y = +parts[2];\n const z = +parts[3];\n\n let frac: Float64Array;\n\n switch (units) {\n case \"crystal\":\n frac = new Float64Array([x, y, z]);\n break;\n\n case \"angstrom\":\n frac = fractional(lattice, new Float64Array([x, y, z]));\n break;\n\n case \"bohr\": {\n // Bohr → angstrom → fractional\n const angstrom = new Float64Array([\n x * BOHR_TO_ANGSTROM,\n y * BOHR_TO_ANGSTROM,\n z * BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n\n case \"alat\": {\n // alat = celldm(1) Bohr → Bohr → angstrom → fractional\n if (celldm[0] === 0) {\n throw new Error(\n \"ATOMIC_POSITIONS alat requires celldm(1) in &SYSTEM\",\n );\n }\n const bohr = new Float64Array([\n x * celldm[0],\n y * celldm[0],\n z * celldm[0],\n ]);\n const angstrom = new Float64Array([\n bohr[0] / BOHR_TO_ANGSTROM,\n bohr[1] / BOHR_TO_ANGSTROM,\n bohr[2] / BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n }\n\n const site: Site = { species: { symbol }, frac };\n\n if (selectiveDynamics && parts.length >= 7) {\n const ifPos = [+parts[4], +parts[5], +parts[6]];\n (site.properties ??= {}).ifPos = ifPos;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n ...(selectiveDynamics ? { selectiveDynamics: true } : {}),\n };\n}\n\n// ---------- internal parsing helpers ----------\n\ninterface CellParamsResult {\n lattice: ReturnType<typeof createLattice>;\n units: string;\n}\n\nfunction parseCellParameters(lines: string[]): CellParamsResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^CELL_PARAMETERS/i.test(line)) {\n const unitMatch = line.match(\n /^CELL_PARAMETERS\\s(?:\\{\|\$)?(\\w+)(?:\\}\|\$)?/i,\n );\n const units = unitMatch?.[1]?.toLowerCase() ?? \"angstrom\";\n\n const rows: number[][] = [];\n for (let j = 1; j <= 3; j++) {\n if (i + j >= lines.length) {\n throw new Error(\"Incomplete CELL_PARAMETERS block\");\n }\n rows.push(lines[i + j].trim().split(/\\s+/).map(Number));\n }\n\n return {\n lattice: createLattice([...rows[0], ...rows[1], ...rows[2]]),\n units,\n };\n }\n }\n\n throw new Error(\"CELL_PARAMETERS block not found\");\n}\n\ninterface AtomBlockResult {\n lines: string[];\n units: AtomCoordMode;\n selectiveDynamics: boolean;\n}\n\nfunction parseAtomicPositions(lines: string[]): AtomBlockResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^ATOMIC_POSITIONS/i.test(line)) {\n const unitMatch = line.match(\n /^ATOMIC_POSITIONS\\s(?:\\{\|\$)?(\\w+)(?:\\}\|\$)?/i,\n );\n const units = (unitMatch?.[1]?.toLowerCase() ??\n \"angstrom\") as AtomCoordMode;\n\n const atomLines: string[] = [];\n\n // check for \"Selective dynamics\" on the NEXT line\n let selectiveDynamics = false;\n let j = i + 1;\n if (j < lines.length && /^selective\\s+dynamics/i.test(lines[j].trim())) {\n selectiveDynamics = true;\n j++;\n }\n\n for (; j < lines.length; j++) {\n const l = lines[j].trim();\n if (!l) break;\n\n const parts = l.split(/\\s+/);\n if (\n parts.length < 4 \|\|\n !/^[A-Za-z]/.test(parts[0]) \|\|\n parts.slice(1, 4).some((x) => Number.isNaN(+x))\n ) {\n break;\n }\n\n atomLines.push(l);\n }\n\n return { lines: atomLines, units, selectiveDynamics };\n }\n }\n\n return { lines: [], units: \"angstrom\", selectiveDynamics: false };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// toPW — data-driven\n// ──────────────────────────────────────────────────────────────────────\n\nconst RESERVED: Record<string, string[]> = {\n CONTROL: [\"title\"],\n};\n\n/** Serializes a Structure to a Quantum ESPRESSO PW input string. /\nexport function toPW(structure: Structure, options?: QEOptions): string {\n const ctrl = { ...QE_DEFAULTS.control, ...options?.control };\n const sys = { ...QE_DEFAULTS.system, ...options?.system };\n const { nat: _nat, ntyp: _ntyp, ibrav: _ibrav, ...sysOpts } = sys;\n const elec = { ...QE_DEFAULTS.electrons, ...options?.electrons };\n\n // --- derive card data from Structure ---\n const speciesOrder = collectSpecies(structure.sites);\n const species = buildAtomicSpecies(speciesOrder, options?.pseudo?.pseudos);\n const positions = buildAtomicPositions(structure);\n const cell = buildCellParameters(structure.lattice);\n const kpoints = buildKPoints(structure, options?.kpoints);\n\n // --- serialize ---\n const lines: string[] = [];\n\n lines.push(`title = '${ctrl.title}'`);\n lines.push(\"\");\n writeNamelist(lines, \"CONTROL\", { ...ctrl, title: undefined });\n lines.push(\"\");\n writeNamelist(lines, \"SYSTEM\", {\n ...sysOpts,\n nat: structure.sites.length,\n ntyp: speciesOrder.length,\n ibrav: 0,\n });\n lines.push(\"\");\n writeNamelist(lines, \"ELECTRONS\", elec);\n lines.push(\"\");\n\n lines.push(...serializeAtomicSpecies(species));\n lines.push(\"\");\n lines.push(...serializeKPoints(kpoints));\n lines.push(\"\");\n lines.push(...serializeCellParameters(cell));\n lines.push(\"\");\n lines.push(\n ...serializeAtomicPositions(positions, structure.selectiveDynamics),\n );\n\n return lines.join(\"\\n\");\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card builders — Structure + options → typed card data\n// ──────────────────────────────────────────────────────────────────────\n\n/* Collect unique species in first-appearance order. /\nfunction collectSpecies(sites: Site[]): string[] {\n const seen = new Set<string>();\n const order: string[] = [];\n for (const site of sites) {\n const sym = site.species.symbol;\n if (!seen.has(sym)) {\n seen.add(sym);\n order.push(sym);\n }\n }\n return order;\n}\n\n/* Build ATOMIC_SPECIES rows from species order + pseudopotential map. /\nfunction buildAtomicSpecies(\n speciesOrder: string[],\n pseudos?: Record<string, string>,\n): AtomicSpeciesEntry[] {\n return speciesOrder.map((symbol) => {\n const el = getElement(symbol);\n return {\n symbol,\n mass: el?.mass ?? 0,\n pseudo: pseudos?.[symbol] ?? `${symbol}.UPF`,\n };\n });\n}\n\n/* Build ATOMIC_POSITIONS rows from Structure sites. /\nfunction buildAtomicPositions(structure: Structure): AtomicPositionEntry[] {\n // group sites by species in first-appearance order\n const grouped = new Map<string, Site[]>();\n for (const site of structure.sites) {\n const sym = site.species.symbol;\n const group = grouped.get(sym);\n if (group) {\n group.push(site);\n } else {\n grouped.set(sym, [site]);\n }\n }\n\n const speciesOrder = collectSpecies(structure.sites);\n const entries: AtomicPositionEntry[] = [];\n\n for (const sym of speciesOrder) {\n const group = grouped.get(sym) ?? [];\n for (const site of group) {\n const entry: AtomicPositionEntry = {\n symbol: sym,\n x: site.frac[0],\n y: site.frac[1],\n z: site.frac[2],\n };\n if (site.properties?.ifPos) {\n entry.ifPos = [\n site.properties.ifPos[0],\n site.properties.ifPos[1],\n site.properties.ifPos[2],\n ];\n }\n entries.push(entry);\n }\n }\n\n return entries;\n}\n\n/* Build CELL_PARAMETERS rows from Lattice. /\nfunction buildCellParameters(\n lattice: Structure[\"lattice\"],\n): CellParameterEntry[] {\n const m = lattice.basis.data;\n return [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ];\n}\n\n/* Build K_POINTS card from options (with kspacing default). /\nfunction buildKPoints(\n structure: Structure,\n kpoints?: QEOptions[\"kpoints\"],\n): KPointsCard {\n if (kpoints) {\n if (\"grid\" in kpoints) {\n return {\n mode: \"automatic\",\n grid: kpoints.grid,\n shift: kpoints.shift ?? [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, kpoints.kspacing),\n shift: [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, QE_DEFAULTS.kpoints.kspacing),\n shift: [0, 0, 0],\n };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card serializers — typed card data → string lines\n// ──────────────────────────────────────────────────────────────────────\n\nfunction serializeAtomicSpecies(entries: AtomicSpeciesEntry[]): string[] {\n const lines = [\"ATOMIC_SPECIES\"];\n for (const e of entries) {\n lines.push(`${e.symbol} ${e.mass} ${e.pseudo}`);\n }\n return lines;\n}\n\nfunction serializeKPoints(card: KPointsCard): string[] {\n switch (card.mode) {\n case \"gamma\":\n return [\"K_POINTS gamma\"];\n case \"automatic\":\n return [\n \"K_POINTS automatic\",\n `${card.grid[0]} ${card.grid[1]} ${card.grid[2]} ${card.shift[0]} ${card.shift[1]} ${card.shift[2]}`,\n ];\n default:\n // list / bands / covering — not used by toPW but handled for completeness\n throw new Error(`K_POINTS mode '${card.mode}' not yet supported in toPW`);\n }\n}\n\nfunction serializeCellParameters(\n entries: CellParameterEntry[],\n unit: \"angstrom\" \| \"bohr\" \| \"alat\" = \"angstrom\",\n): string[] {\n const lines = [`CELL_PARAMETERS ${unit}`];\n for (const [a, b, c] of entries) {\n lines.push(`${a} ${b} ${c}`);\n }\n return lines;\n}\n\nfunction serializeAtomicPositions(\n entries: AtomicPositionEntry[],\n selectiveDynamics?: boolean,\n unit: \"crystal\" \| \"angstrom\" \| \"bohr\" \| \"alat\" = \"crystal\",\n): string[] {\n const lines = [`ATOMIC_POSITIONS ${unit}`];\n if (selectiveDynamics) {\n lines.push(\"Selective dynamics\");\n }\n for (const e of entries) {\n let suffix = \"\";\n if (e.ifPos) {\n suffix = ` ${e.ifPos[0]} ${e.ifPos[1]} ${e.ifPos[2]}`;\n }\n lines.push(`${e.symbol} ${e.x} ${e.y} ${e.z}${suffix}`);\n }\n return lines;\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Namelist serializer — generic key → value\n// ──────────────────────────────────────────────────────────────────────\n\nfunction writeNamelist(\n lines: string[],\n name: string,\n params: Record<string, unknown>,\n): void {\n const reserved = new Set(RESERVED[name] ?? []);\n const entries = Object.entries(params).filter(\n ([k, v]) => !reserved.has(k) && v !== undefined,\n );\n if (entries.length === 0) {\n lines.push(`&${name}`);\n lines.push(\"/\");\n return;\n }\n lines.push(`&${name}`);\n for (const [key, value] of entries) {\n if (typeof value === \"string\") {\n lines.push(` ${key} = '${value}'`);\n } else if (typeof value === \"boolean\") {\n lines.push(` ${key} = .${value ? \"TRUE\" : \"FALSE\"}.`);\n } else if (typeof value === \"number\" && !Number.isFinite(value)) {\n continue;\n } else {\n lines.push(` ${key} = ${value}`);\n }\n }\n lines.push(\"/\");\n}\n","import type {\n KGrid,\n KPath,\n KPointSet,\n KPoints,\n Vec3,\n} from \"../../kpoints/kpoints\";\nimport type { KPointsBands, KPointsCard, KPointsList, Kpt } from \"../pw/schema/cards\";\n\nconst K_POINTS_HEADER = /^K_POINTS(?:\\s+\\{?\$?(\\w+)\$?\\}?)?/i;\nconst NEXT_CARD =\n /^(?:ATOMIC_SPECIES\|ATOMIC_POSITIONS\|CELL_PARAMETERS\|K_POINTS\|ADDITIONAL_K_POINTS\|OCCUPATIONS\|CONSTRAINTS\|ATOMIC_VELOCITIES\|ATOMIC_FORCES\|HUBBARD\|SOLVENTS)\\b/i;\n\nfunction stripComment(line: string): string {\n let cut = line.length;\n const bang = line.indexOf(\"!\");\n const hash = line.indexOf(\"#\");\n if (bang !== -1) cut = Math.min(cut, bang);\n if (hash !== -1) cut = Math.min(cut, hash);\n return line.slice(0, cut);\n}\n\nfunction toNumbers(line: string): number[] {\n return stripComment(line)\n .split(/\\s+/)\n .filter((t) => t !== \"\")\n .map(Number);\n}\n\nfunction parseKpt(line: string): Kpt {\n const n = toNumbers(line);\n if (n.length < 4) {\n throw new Error(`Invalid K_POINTS line: ${line}`);\n }\n return { x: n[0], y: n[1], z: n[2], w: n[3] };\n}\n\nfunction parsePointList(rest: string[]): Kpt[] {\n const count = Number.parseInt(rest[0] ?? \"\", 10);\n if (Number.isNaN(count)) {\n throw new Error(\"K_POINTS list requires a point count\");\n }\n const pointLines = rest.slice(1, 1 + count);\n if (pointLines.length !== count) {\n throw new Error(`Expected ${count} k-points, got ${pointLines.length}`);\n }\n return pointLines.map(parseKpt);\n}\n\n/* Extract the K_POINTS card block from a pw.x input. /\nfunction extractKPointsBlock(text: string): string[] {\n const lines = text.split(\"\\n\");\n let start = -1;\n\n for (let i = 0; i < lines.length; i++) {\n if (K_POINTS_HEADER.test(lines[i].trim())) {\n start = i;\n break;\n }\n }\n\n if (start === -1) {\n throw new Error(\"K_POINTS card not found\");\n }\n\n const block = [lines[start].trim()];\n\n for (let i = start + 1; i < lines.length; i++) {\n const l = lines[i].trim();\n if (l === \"\" \|\| NEXT_CARD.test(l)) break;\n block.push(l);\n }\n\n return block;\n}\n\n/* Parse the K_POINTS card of a Quantum ESPRESSO pw.x input into typed card data. /\nexport function fromPWKPoints(text: string): KPointsCard {\n const block = extractKPointsBlock(text);\n const modeMatch = block[0].match(K_POINTS_HEADER);\n const mode = (modeMatch?.[1]?.toLowerCase() ??\n \"automatic\") as KPointsCard[\"mode\"];\n const rest = block.slice(1);\n\n switch (mode) {\n case \"automatic\": {\n const n = toNumbers(rest[0] ?? \"\");\n if (n.length < 6) {\n throw new Error(\"K_POINTS automatic requires 6 numbers\");\n }\n return {\n mode,\n grid: [n[0], n[1], n[2]],\n shift: [n[3], n[4], n[5]],\n };\n }\n case \"gamma\":\n return { mode };\n case \"crystal\":\n case \"tpiba\":\n return { mode, points: parsePointList(rest) };\n case \"crystal_b\":\n case \"tpiba_b\": {\n const nks = Number.parseInt(rest[0] ?? \"\", 10);\n if (Number.isNaN(nks)) {\n throw new Error(\"K_POINTS band path requires nks\");\n }\n const pointLines = rest.slice(1, 1 + nks);\n if (pointLines.length !== nks) {\n throw new Error(\n `Expected ${nks} k-points, got ${pointLines.length}`,\n );\n }\n return { mode, nks, points: pointLines.map(parseKpt) };\n }\n case \"crystal_c\":\n case \"tpiba_c\":\n return { mode, points: parsePointList(rest) };\n default:\n throw new Error(`Unsupported K_POINTS mode '${mode}'`);\n }\n}\n\nfunction serializeKpt(k: Kpt): string {\n return `${k.x} ${k.y} ${k.z} ${k.w}`;\n}\n\nfunction serializeList(card: {\n mode: \"crystal\" \| \"tpiba\" \| \"crystal_c\" \| \"tpiba_c\";\n points: Kpt[];\n}): string {\n return [\n `K_POINTS ${card.mode}`,\n String(card.points.length),\n ...card.points.map(serializeKpt),\n ].join(\"\\n\");\n}\n\n/* Serialize K_POINTS card data back to a Quantum ESPRESSO pw.x card. /\nexport function toPWKPoints(card: KPointsCard): string {\n switch (card.mode) {\n case \"gamma\":\n return \"K_POINTS gamma\";\n case \"automatic\":\n return `K_POINTS automatic\\n${card.grid.join(\" \")} ${card.shift.join(\" \")}`;\n case \"crystal\":\n case \"tpiba\":\n return serializeList(card);\n case \"crystal_b\":\n case \"tpiba_b\":\n return [\n `K_POINTS ${card.mode}`,\n String(card.nks),\n ...card.points.map(serializeKpt),\n ].join(\"\\n\");\n case \"crystal_c\":\n case \"tpiba_c\":\n return serializeList(card);\n }\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Canonical k-point conversions\n// ──────────────────────────────────────────────────────────────────────\n\n/* Default number of k-points interpolated per band-path segment. /\nconst DEFAULT_POINTS_PER_SEGMENT = 40;\n\nfunction pointListToKPointSet(\n mode: \"crystal\" \| \"tpiba\" \| \"crystal_c\" \| \"tpiba_c\",\n points: readonly Kpt[],\n): KPointSet {\n const reciprocal =\n mode === \"crystal\" \|\| mode === \"crystal_c\" ? \"reciprocal\" : \"cartesian\";\n return {\n kind: \"points\",\n points: points.map((k) => ({ coordinate: [k.x, k.y, k.z] as const })),\n weights: points.map((k) => k.w),\n coordinateSystem: reciprocal,\n };\n}\n\nfunction pathFromBandPoints(points: readonly Kpt[]): KPath {\n if (points.length < 2) {\n throw new Error(\"K_POINTS band path requires at least two points\");\n }\n const names = new Map<string, string>();\n const named: Record<string, Vec3> = {};\n const nameFor = (k: Kpt): string => {\n const key = [k.x, k.y, k.z].join(\" \");\n let name = names.get(key);\n if (name === undefined) {\n name = `k${names.size + 1}`;\n names.set(key, name);\n named[name] = [k.x, k.y, k.z];\n }\n return name;\n };\n const segments: [string, string][] = [];\n for (let i = 0; i < points.length - 1; i++) {\n segments.push([nameFor(points[i]), nameFor(points[i + 1])]);\n }\n\n // Extract density: the weight of each vertex (except the last) is the\n // number of intermediate k-points on the segment to the next vertex.\n // If all segment weights are equal, set KPath.density.\n const segmentWeights = points.slice(0, -1).map((k) => k.w);\n const density =\n segmentWeights.length > 0 &&\n segmentWeights.every((w) => w === segmentWeights[0])\n ? segmentWeights[0]\n : undefined;\n\n return { kind: \"path\", points: named, segments, density };\n}\n\n/\n Read the K_POINTS card of a Quantum ESPRESSO pw.x input and convert it to\n * the canonical k-point representation.\n \n The pw.x card may appear on its own or embedded in a full pw.in file.\n \n - automatic grids map to {@link KGrid} (mesh + origin, origin being the shift)\n * - crystal / crystal_c and tpiba / tpiba_c lists map to {@link KPointSet}\n * - crystal_b band paths map to {@link KPath} (tpiba_b needs a lattice and\n * is not supported)\n /\nexport function kpointsFromPW(text: string): KPoints {\n const card = fromPWKPoints(text);\n\n switch (card.mode) {\n case \"automatic\":\n return {\n kind: \"grid\",\n mesh: card.grid,\n origin: card.shift,\n scheme: \"gamma-centered\",\n };\n case \"gamma\":\n return {\n kind: \"grid\",\n mesh: [1, 1, 1],\n origin: [0, 0, 0],\n scheme: \"gamma-centered\",\n };\n case \"crystal\":\n case \"tpiba\":\n case \"crystal_c\":\n case \"tpiba_c\":\n return pointListToKPointSet(card.mode, card.points);\n case \"crystal_b\":\n return pathFromBandPoints(card.points);\n case \"tpiba_b\":\n throw new Error(\n \"tpiba_b band paths are expressed in 2pi/alat units; converting them requires a lattice\",\n );\n }\n}\n\nfunction pathToBandCard(\n path: KPath,\n pointsPerSegment: number,\n): KPointsBands {\n const vertices: Kpt[] = [];\n // Build the vertex list in segment order (shared endpoints collapse naturally)\n for (const [start, stop] of path.segments) {\n const s = path.points[start];\n if (!s) {\n throw new Error(`KPath references unknown point '${start}'`);\n }\n vertices.push({ x: s[0], y: s[1], z: s[2], w: pointsPerSegment });\n }\n const last = path.segments[path.segments.length - 1];\n if (last) {\n const end = path.points[last[1]];\n if (!end) {\n throw new Error(`KPath references unknown point '${last[1]}'`);\n }\n // Last vertex weight is ignored by pw.x; write 1 by convention.\n vertices.push({ x: end[0], y: end[1], z: end[2], w: 1 });\n }\n return { mode: \"crystal_b\", nks: vertices.length, points: vertices };\n}\n\nfunction kPointSetToListCard(set: KPointSet): KPointsList {\n const cartesian = set.coordinateSystem === \"cartesian\";\n return {\n mode: cartesian ? \"tpiba\" : \"crystal\",\n points: set.points.map((p, i) => ({\n x: p.coordinate[0],\n y: p.coordinate[1],\n z: p.coordinate[2],\n w: set.weights?.[i] ?? 1,\n })),\n };\n}\n\n/*\n Serialize canonical k-point data as a K_POINTS card block, ready to be\n * embedded in a Quantum ESPRESSO pw.x input file.\n \n - grids are written in automatic (Monkhorst-Pack) mode\n * - k-point sets are written as crystal (reciprocal) or tpiba (2pi/alat)\n lists, depending on their coordinate system\n * - paths are written as crystal_b band paths; `pointsPerSegment` (default\n * 40) sets the number of k-points interpolated along each segment.\n * When `pointsPerSegment` is omitted, the path's own `density` is used\n * if set, otherwise the default.\n * High-symmetry point names are written as inline comments.\n /\nexport function kpointsToPW(\n data: KPoints,\n pointsPerSegment?: number,\n): string {\n switch (data.kind) {\n case \"grid\":\n return toPWKPoints({\n mode: \"automatic\",\n grid: [...data.mesh],\n shift: [...data.origin],\n });\n case \"path\": {\n const density =\n pointsPerSegment !== undefined\n ? Math.max(1, Math.round(pointsPerSegment))\n : data.density !== undefined\n ? Math.max(1, Math.round(data.density))\n : DEFAULT_POINTS_PER_SEGMENT;\n return pathWithComments(data, density);\n }\n case \"points\":\n return toPWKPoints(kPointSetToListCard(data));\n }\n}\n\n/\n Serialize a KPath as a crystal_b card with high-symmetry point name comments.\n /\nfunction pathWithComments(path: KPath, density: number): string {\n // Build the vertex list in segment order (shared endpoints collapse naturally)\n const vertices: { x: number; y: number; z: number; label: string; w: number }[] = [];\n const seen = new Set<string>();\n for (let si = 0; si < path.segments.length; si++) {\n const [start, stop] = path.segments[si];\n const s = path.points[start];\n if (!s) {\n throw new Error(`KPath references unknown point '${start}'`);\n }\n const sKey = start;\n if (!seen.has(sKey)) {\n seen.add(sKey);\n vertices.push({ x: s[0], y: s[1], z: s[2], label: start, w: density });\n }\n }\n const last = path.segments[path.segments.length - 1];\n if (last) {\n const end = path.points[last[1]];\n if (!end) {\n throw new Error(`KPath references unknown point '${last[1]}'`);\n }\n // Last vertex weight is ignored by pw.x; write 1 by convention.\n vertices.push({ x: end[0], y: end[1], z: end[2], label: last[1], w: 1 });\n }\n\n const lines = [`K_POINTS crystal_b`, String(vertices.length)];\n for (const v of vertices) {\n lines.push(`${v.x} ${v.y} ${v.z} ${v.w} ! ${v.label}`);\n }\n return lines.join(\"\\n\");\n}\n","import type {\n GridShape,\n Vec3,\n KGrid,\n KPath,\n KPoint,\n KPointSet,\n KPoints,\n} from \"../../kpoints/kpoints\";\nimport { LineReader } from \"../helpers\";\n\n/* Comment line written for automatic-mesh output. /\nconst GRID_COMMENT = \"Automatic mesh\";\n/* Comment line written for explicit-list output. /\nconst LIST_COMMENT = \"K-points list\";\n\n/\n Parse a VASP KPOINTS file.\n \n Automatic subdivision meshes (line 2 is \"0\") become a {@link KGrid}; explicit\n * k-point lists (line 2 is a positive count) become a {@link KPointSet}; line\n * modes (line 2 is a count with a \"Line-mode\" scheme, or a negative count)\n * become a {@link KPath}. The deprecated fully-automatic mode errors out.\n /\nexport function fromKPOINTS(text: string): KPoints {\n const r = new LineReader(text);\n\n // The first line is a free-form comment. Skip any leading blank lines,\n // though there should not be any.\n let line = r.next();\n while (line !== null && line.trim() === \"\") {\n line = r.next();\n }\n if (line === null) {\n throw new Error(\"KPOINTS file is too short\");\n }\n\n const mode = r.nextTrimmed();\n const modeNumber = Number(mode);\n if (mode === \"0\") {\n return parseAutomaticMesh(r);\n }\n if (Number.isInteger(modeNumber)) {\n const scheme = r.nextTrimmed();\n // A negative count is the legacy line-mode marker; a \"Line-mode\" scheme\n // line marks the current one.\n if (scheme.toLowerCase().startsWith(\"l\") \|\| modeNumber < 0) {\n return parseLineMode(r, scheme, modeNumber < 0, Math.abs(modeNumber));\n }\n return parseExplicitList(r, scheme, modeNumber);\n }\n throw new Error(`Unsupported KPOINTS mode '${mode}'`);\n}\n\n/* Parse an automatic subdivision (mesh) card. /\nfunction parseAutomaticMesh(r: LineReader): KGrid {\n const scheme = r.nextTrimmed();\n const first = scheme.toLowerCase();\n if (first.startsWith(\"a\")) {\n throw new Error(\"KPOINTS fully-automatic mode is not yet supported\");\n }\n const monkhorstPack = first.startsWith(\"m\");\n\n const mesh = parseVec3(r.nextTrimmed(), \"mesh\");\n\n // The shift line is optional and defaults to no shift.\n const shiftLine = r.next();\n const shift: Vec3 =\n shiftLine === null \|\| shiftLine.trim() === \"\"\n ? [0, 0, 0]\n : parseVec3(shiftLine.trim(), \"shift\");\n\n return {\n kind: \"grid\",\n mesh,\n origin: monkhorstPack ? monkhorstOrigin(mesh, shift) : shift,\n scheme: monkhorstPack ? \"monkhorst-pack\" : \"gamma-centered\",\n };\n}\n\n/* Parse an explicit k-point list. /\nfunction parseExplicitList(\n r: LineReader,\n scheme: string,\n count: number,\n): KPointSet {\n const coordinateSystem = parseCoordinateSystem(scheme);\n\n const points: KPoint[] = [];\n const weights: number[] = [];\n for (let i = 0; i < count; i++) {\n const { coordinate, weight } = parsePointLine(r.nextTrimmed());\n points.push({ coordinate });\n weights.push(weight);\n }\n\n return { kind: \"points\", points, weights, coordinateSystem };\n}\n\n/\n Parse a line-mode band path. `legacyScheme` marks files where the line after\n * the (negative) count is already the coordinate system line.\n \n Coordinates are stored in the canonical fractional reciprocal form; Cartesian\n * input cannot be converted without the lattice and is rejected.\n /\nfunction parseLineMode(\n r: LineReader,\n scheme: string,\n legacyScheme: boolean,\n pointsPerLine: number,\n): KPath {\n const coordinateSystem = parseCoordinateSystem(\n legacyScheme ? scheme : r.nextTrimmed(),\n );\n if (coordinateSystem === \"cartesian\") {\n throw new Error(\n \"KPOINTS Cartesian line-mode is not yet supported\",\n );\n }\n\n // Group the remaining lines into blank-line-separated blocks, each block\n // holding the points of one or more segments (two lines per segment).\n const blocks: string[][] = [];\n let current: string[] = [];\n let line: string \| null;\n while ((line = r.next()) !== null) {\n const trimmed = line.trim();\n if (trimmed === \"\") {\n if (current.length > 0) {\n blocks.push(current);\n current = [];\n }\n } else {\n current.push(trimmed);\n }\n }\n if (current.length > 0) {\n blocks.push(current);\n }\n\n const points: Record<string, Vec3> = {};\n const segments: [string, string][] = [];\n let autoName = 0;\n\n for (const block of blocks) {\n if (block.length % 2 !== 0) {\n throw new Error(\"KPOINTS line-mode segments must come in pairs of lines\");\n }\n for (let i = 0; i < block.length; i += 2) {\n const start = registerPathPoint(points, parsePathPoint(block[i]), ++autoName);\n const stop = registerPathPoint(points, parsePathPoint(block[i + 1]), ++autoName);\n segments.push([start, stop]);\n }\n }\n\n const density =\n Number.isFinite(pointsPerLine) && pointsPerLine > 0\n ? Math.round(pointsPerLine)\n : undefined;\n\n return { kind: \"path\", points, segments, density };\n}\n\n/* Parse a line-mode point row: x y z [label]; labels may follow \"!\". /\nfunction parsePathPoint(line: string): {\n coordinate: Vec3;\n label?: string;\n} {\n const bang = line.indexOf(\"!\");\n const content = bang === -1 ? line : line.slice(0, bang);\n const comment = bang === -1 ? \"\" : line.slice(bang + 1).trim();\n\n const tokens = content.trim().split(/\\s+/);\n if (tokens.length < 3 \|\| tokens.length > 4) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n const values = tokens.slice(0, 3).map(Number);\n if (values.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n return {\n coordinate: [values[0], values[1], values[2]],\n label: comment \|\| tokens[3],\n };\n}\n\n/* Register a path point by name, auto-naming unlabeled points. /\nfunction registerPathPoint(\n points: Record<string, Vec3>,\n point: { coordinate: Vec3; label?: string },\n autoName: number,\n): string {\n const name = point.label ?? `k${autoName}`;\n const existing = points[name];\n if (existing !== undefined && !vecApproxEqual(existing, point.coordinate)) {\n throw new Error(\n `KPOINTS label '${name}' is used for two different k-points`,\n );\n }\n points[name] = point.coordinate;\n return name;\n}\n\nfunction vecApproxEqual(a: Vec3, b: Vec3): boolean {\n return a.every((x, i) => Math.abs(x - b[i]) < 1e-9);\n}\n\n/* Parse a coordinate system name (full or abbreviated, any case). /\nfunction parseCoordinateSystem(line: string): KPointSet[\"coordinateSystem\"] {\n const cs = line.toLowerCase();\n if (cs === \"reciprocal\" \|\| cs === \"frac\" \|\| cs === \"r\") return \"reciprocal\";\n if (cs === \"cartesian\" \|\| cs === \"cart\" \|\| cs === \"c\") return \"cartesian\";\n throw new Error(`Unknown KPOINTS coordinate system '${line}'`);\n}\n\n/\n Parse a single k-point row: x y z [weight] [label]. The weight defaults to 1\n * and a trailing label (as produced by some generators) is ignored.\n /\nfunction parsePointLine(line: string): { coordinate: Vec3; weight: number } {\n const tokens = line.split(/\\s+/);\n if (tokens.length < 3) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n const values = tokens.map(Number);\n const required = tokens.length >= 4 ? values.slice(0, 4) : values.slice(0, 3);\n if (required.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n return {\n coordinate: [values[0], values[1], values[2]],\n weight: tokens.length >= 4 ? values[3] : 1,\n };\n}\n\n/* Parse a line of three numbers, e.g. the mesh or shift row. /\nfunction parseVec3(line: string, what: string): Vec3 {\n const values = line.split(/\\s+/).map(Number);\n if (values.length !== 3 \|\| values.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS ${what}: '${line}'`);\n }\n return [values[0], values[1], values[2]];\n}\n\n/\n Offset applied to each axis so a Monkhorst-Pack grid is symmetric about the\n * origin. KGrid index [i, j, k] sits at origin + [i/nx, j/ny, k/nz], while MP\n * points are at (2i - n - 1) / 2n, so the origin is (1 - n) / 2n per axis.\n /\nfunction monkhorstOrigin(mesh: GridShape, shift: Vec3): Vec3 {\n const offset = (n: number, s: number) => (1 - n) / (2 n) + s;\n return [\n offset(mesh[0], shift[0]),\n offset(mesh[1], shift[1]),\n offset(mesh[2], shift[2]),\n ];\n}\n\n/*\n Serialize k-point data back to a VASP KPOINTS file.\n \n Grids are written as automatic subdivision meshes. K-point sets are\n * canonicalized to a mesh when their points form a regular grid with uniform\n * weights (only in reciprocal coordinates); otherwise they are written as an\n * explicit list. Paths are written in reciprocal line mode, interpolating\n * `pointsPerLine` k-points per segment (default 40 when omitted; falls back\n * to `KPath.density` if set).\n /\nexport function toKPOINTS(\n data: KPoints,\n pointsPerLine?: number,\n): string {\n switch (data.kind) {\n case \"grid\":\n return serializeGrid(data);\n case \"path\":\n return serializePath(data, pointsPerLine);\n case \"points\":\n return serializePointSet(data);\n }\n}\n\n/\n Serialize a mesh, inferring the scheme from the origin: a grid whose origin\n * is the canonical Monkhorst-Pack offset (1 - n) / 2n for its mesh is written\n * as a Monkhorst-Pack file, anything else as a Gamma-centered file with the\n * origin as the shift. Either way the generated k-point mesh is identical.\n /\nfunction serializeGrid({ mesh, origin, scheme }: KGrid): string {\n const shift = scheme === \"monkhorst-pack\" ? [0, 0, 0] : origin;\n\n return [\n GRID_COMMENT,\n \"0\",\n scheme === \"monkhorst-pack\" ? \"Monkhorst-Pack\" : \"Gamma\",\n mesh.join(\" \"),\n shift.join(\" \"),\n ].join(\"\\n\");\n}\n\n/* Serialize an explicit k-point list, canonicalizing to a mesh if possible. /\nfunction serializePointSet(data: KPointSet): string {\n const grid = detectGrid(data);\n if (grid) {\n return serializeGrid(grid);\n }\n\n const coordinateSystem =\n data.coordinateSystem === \"cartesian\" ? \"Cartesian\" : \"Reciprocal\";\n const rows = data.points.map(\n (p, i) => `${p.coordinate.join(\" \")} ${data.weights?.[i] ?? 1}`,\n );\n\n return [\n LIST_COMMENT,\n String(data.points.length),\n coordinateSystem,\n ...rows,\n ].join(\"\\n\");\n}\n\n/\n Serialize a band path in reciprocal line mode. The number of points per line\n * is not part of {@link KPath} and is written with this default.\n /\nconst DEFAULT_POINTS_PER_LINE = 40;\n\nfunction serializePath(\n { points, segments, density: pathDensity }: KPath,\n pointsPerLine?: number,\n): string {\n const density =\n pointsPerLine !== undefined\n ? Math.max(1, Math.round(pointsPerLine))\n : pathDensity !== undefined\n ? Math.max(1, Math.round(pathDensity))\n : DEFAULT_POINTS_PER_LINE;\n\n const rows: string[] = [];\n for (const [start, stop] of segments) {\n rows.push(`${points[start].join(\" \")} ${start}`);\n rows.push(`${points[stop].join(\" \")} ${stop}`);\n rows.push(\"\");\n }\n rows.pop();\n\n return [\n \"Band path\",\n String(density),\n \"Line-mode\",\n \"Reciprocal\",\n ...rows,\n ].join(\"\\n\");\n}\n\n/\n Detect whether a reciprocal-coordinate point set is a regular grid.\n * Returns the grid, or null if the set is not a uniform mesh (non-uniform\n * weights, Cartesian coordinates, or irregular point spacing).\n /\nfunction detectGrid(data: KPointSet): KGrid \| null {\n if (data.coordinateSystem === \"cartesian\") return null;\n\n const weights = data.weights;\n if (weights && !weights.every((w) => Math.abs(w - weights[0]) < 1e-12)) {\n return null;\n }\n\n const axes: number[][] = [[], [], []];\n for (const { coordinate } of data.points) {\n for (let i = 0; i < 3; i++) {\n if (!axes[i].some((u) => Math.abs(u - coordinate[i]) < 1e-12)) {\n axes[i].push(coordinate[i]);\n }\n }\n }\n for (const axis of axes) {\n axis.sort((a, b) => a - b);\n }\n\n const mesh: GridShape = [axes[0].length, axes[1].length, axes[2].length];\n if (mesh[0] mesh[1] * mesh[2] !== data.points.length) return null;\n\n // Each axis must be evenly spaced with step 1/n from the first value.\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < mesh[i]; j++) {\n if (Math.abs(axes[i][j] - (axes[i][0] + j / mesh[i])) > 1e-9) {\n return null;\n }\n }\n }\n\n return {\n kind: \"grid\",\n mesh,\n origin: [axes[0][0], axes[1][0], axes[2][0]],\n scheme: \"gamma-centered\",\n };\n}\n","import type { KPath, KPoints, Vec3 } from \"../../kpoints/kpoints\";\n\n// ──────────────────────────────────────────────────────────────────────\n// CRYSTAL D3 BAND format\n// https://www.crystal.unito.it/Manuals/crystal17.pdf\n//\n// Format (for a band-structure path), per the CRYSTAL manual and\n// https://tutorials.crystalsolutions.eu (keyword BAND):\n// BAND\n// <title>\n// <nseg> <ISHR> <totk> <first_band> <last_band> <write_unit25> <print> !<comment>\n// x1 y1 z1 x2 y2 z2 !Segment_name\n// ...\n//\n// Header numbers:\n// nseg number of segments in the reciprocal-space path\n// ISHR shrinking factor; segment coordinates are multiples of 1/ISHR\n// totk total number of k points along the path\n// first_band first band to be saved\n// last_band last band to be saved\n// write_unit25 if 1, write the bands on fortran unit 25\n// print printing options\n//\n// Each segment line has 6 reciprocal-space coordinates (start, end)\n// followed by an optional `!` comment indicating the segment label.\n// The first header number is the number of segment lines.\n// ──────────────────────────────────────────────────────────────────────\n\nconst BAND_HEADER = /^BAND\\s$/i;\n\n/* Default number of k-points interpolated per band-path segment. /\nconst DEFAULT_POINTS_PER_SEGMENT = 40;\n\nfunction stripComment(line: string): string {\n let cut = line.length;\n const bang = line.indexOf(\"!\");\n const hash = line.indexOf(\"#\");\n if (bang !== -1) cut = Math.min(cut, bang);\n if (hash !== -1) cut = Math.min(cut, hash);\n return line.slice(0, cut).trim();\n}\n\nfunction extractComment(line: string): string {\n const bang = line.indexOf(\"!\");\n const content = bang === -1 ? line : line.slice(0, bang);\n const explicit = bang === -1 ? \"\" : line.slice(bang + 1).trim();\n if (explicit !== \"\") return explicit;\n\n // No `!` marker: any tokens after the first six (the segment coordinates)\n // are treated as the segment label, e.g. \"GAMMA -> C\".\n const tokens = content.trim().split(/\\s+/).filter((t) => t !== \"\");\n for (let i = 6; i < tokens.length; i++) {\n if (!NUMERIC_TOKEN.test(tokens[i])) {\n return tokens.slice(i).join(\" \");\n }\n }\n return \"\";\n}\n\nconst NUMERIC_TOKEN = /^[-+]?\\d\\.?\\d+(?:[eE][-+]?\\d+)?$/;\n\nfunction parseVec6(line: string): [Vec3, Vec3] {\n const stripped = stripComment(line);\n const tokens = stripped.split(/\\s+/).filter(Boolean);\n if (tokens.length < 6) {\n throw new Error(`Invalid D3 BAND segment line: '${line}'`);\n }\n const nums = tokens.slice(0, 6).map(Number);\n if (nums.some(Number.isNaN)) {\n throw new Error(`Invalid D3 BAND segment line: '${line}'`);\n }\n return [\n [nums[0], nums[1], nums[2]],\n [nums[3], nums[4], nums[5]],\n ];\n}\n\nfunction formatVec6(start: Vec3, end: Vec3, comment: string): string {\n const cmt = comment ? ` ${comment}` : \"\";\n return `${start.join(\" \")} ${end.join(\" \")}${cmt}`;\n}\n\n/*\n Parse a CRYSTAL D3 BAND input file into the canonical k-point representation.\n \n Segments are returned as a {@link KPath}. Coordinates are in reciprocal\n * lattice units (2π/a); converting to fractional coordinates requires the\n * lattice. The returned path stores the raw coordinates.\n \n @param text The D3 BAND file content.\n /\nexport function fromCrystalD3(text: string): KPath {\n // Only trim leading/trailing blank lines: an empty title line is valid\n // and must stay in its slot (line 2).\n const raw = text.split(\"\\n\");\n let first = 0;\n let last = raw.length - 1;\n while (first < raw.length && raw[first].trim() === \"\") first++;\n while (last > first && raw[last].trim() === \"\") last--;\n const lines = raw.slice(first, last + 1);\n\n if (lines.length < 3) {\n throw new Error(\"D3 BAND file is too short\");\n }\n\n if (!BAND_HEADER.test(lines[0].trim())) {\n throw new Error(\"D3 BAND file must start with 'BAND'\");\n }\n\n // Line 2: title (ignored for canonical representation)\n const _title = lines[1].trim();\n\n // Line 3: header — first number is the number of segments\n const headerNums = stripComment(lines[2])\n .split(/\\s+/)\n .filter(Boolean)\n .map(Number);\n if (headerNums.length < 1 \|\| headerNums.some(Number.isNaN)) {\n throw new Error(\"Invalid D3 BAND header line\");\n }\n const nks = headerNums[0];\n\n if (lines.length < 3 + nks) {\n throw new Error(\n `D3 BAND header declares ${nks} segments but only ${lines.length - 3} lines remain`,\n );\n }\n\n const points: Record<string, Vec3> = {};\n const nameByCoord = new Map<string, string>();\n const segments: [string, string][] = [];\n let autoName = 0;\n\n const nameFor = (coord: Vec3, preferred?: string): string => {\n const key = coord.join(\" \");\n const existing = nameByCoord.get(key);\n if (existing !== undefined) return existing;\n if (preferred !== undefined) {\n const prev = points[preferred];\n if (prev !== undefined && !vecApproxEqual(prev, coord)) {\n throw new Error(\n `D3 BAND: label '${preferred}' used for two different coordinates`,\n );\n }\n nameByCoord.set(key, preferred);\n points[preferred] = coord;\n return preferred;\n }\n const name = `k${++autoName}`;\n nameByCoord.set(key, name);\n points[name] = coord;\n return name;\n };\n\n for (let i = 3; i < 3 + nks; i++) {\n const line = lines[i];\n const [start, end] = parseVec6(line);\n const comment = extractComment(line);\n\n // Parse comment like \"GAMMA -> C\" or \"C_2 -> Y_2\"\n let startName: string \| undefined;\n let endName: string \| undefined;\n if (comment.includes(\"->\")) {\n const parts = comment.split(\"->\").map((s) => s.trim());\n startName = parts[0] \|\| undefined;\n endName = parts[1] \|\| undefined;\n }\n\n segments.push([\n nameFor(start, startName),\n nameFor(end, endName),\n ]);\n }\n\n return { kind: \"path\", points, segments };\n}\n\nfunction vecApproxEqual(a: Vec3, b: Vec3): boolean {\n return a.every((x, i) => Math.abs(x - b[i]) < 1e-6);\n}\n\n/\n Serialize canonical k-point data as a CRYSTAL D3 BAND input file.\n \n The path segments are written as start/end coordinate pairs with inline\n * segment name comments. The header line follows the CRYSTAL BAND format:\n * segment count, shrinking factor 1 (fractional reciprocal coordinates),\n * the total number of k points (segments × points per segment), a\n * 1st-to-0th band range, unit-25 writing on, and no printing options.\n \n @param data The canonical k-point data. Must be a {@link KPath}.\n * @param title Optional title line (defaults to empty).\n * @param pointsPerSegment Number of k points interpolated per segment.\n * Defaults to the path's own `density` when set,\n * otherwise 40.\n /\nexport function toCrystalD3(\n data: KPoints,\n title = \"\",\n pointsPerSegment?: number,\n): string {\n if (data.kind !== \"path\") {\n throw new Error(\"toCrystalD3 only supports KPath data\");\n }\n\n const segmentLines: string[] = [];\n for (const [startName, endName] of data.segments) {\n const start = data.points[startName];\n const end = data.points[endName];\n if (!start \|\| !end) {\n throw new Error(\n `KPath references unknown point '${startName}' or '${endName}'`,\n );\n }\n segmentLines.push(formatVec6(start, end, `${startName} -> ${endName}`));\n }\n\n const nseg = data.segments.length;\n const density =\n pointsPerSegment !== undefined\n ? Math.max(1, Math.round(pointsPerSegment))\n : data.density !== undefined\n ? Math.max(1, Math.round(data.density))\n : DEFAULT_POINTS_PER_SEGMENT;\n\n // TODO(check): CRYSTAL's exact joint-dedup rule for the total k-point count\n // is unverified. nseg × points-per-segment matches the MgO tutorial\n // (4 segments → 60 total = 4 × 15) and mirrors the VASP/QE density semantics.\n const totalPoints = nseg density;\n // [nseg, ISHR=1, totk, first_band, last_band, write_unit25, print]\n const header = `${nseg} 1 ${totalPoints} 1 0 1 0`;\n\n return [\"BAND\", title, header, ...segmentLines].join(\"\\n\");\n}\n","/*\n First-class pseudopotential data model.\n \n This module defines the canonical in-memory representation of a\n * pseudopotential. The model is derived from the UPF v2.0.1 format (the\n * superset of all supported formats) and every other format is handled by an\n * adapter in `lib/core/io/pseudo/` that converts into / out of this type.\n \n Canonical in-memory units: Rydberg (energy), Bohr (length) — i.e. the\n * UPF-native units. Adapters for Hartree-based formats (PSP8, FHI/CPI, PSML,\n * GTH) convert energies on parse (×2) and back on serialize (×0.5). Both\n * factors are exact powers of two, so round-trips stay bit-exact.\n /\n\n/* Pseudopotential type identifiers in UPF format. /\nexport type PseudopotentialType = \"NC\" \| \"SL\" \| \"1/r\" \| \"US\" \| \"PAW\";\n\n/* Relativistic treatment identifiers. \"no\" is observed in the wild (FHI98PP). /\nexport type RelativisticType = \"scalar\" \| \"full\" \| \"nonrelativistic\" \| \"no\";\n\n/* UPF version string. Only set when the source format is UPF. /\nexport type UPFVersion = \"1.0.0\" \| \"2.0.1\";\n\n/* Source format identifier for interconversion. /\nexport type PseudopotentialFormat =\n \| \"UPF1\"\n \| \"UPF2\"\n \| \"PSP8\"\n \| \"PSML\"\n \| \"CPI\"\n \| \"GTH\"\n \| \"HGH\";\n\n/* Canonical in-memory energy unit (Rydberg). /\nexport type EnergyUnit = \"Ry\";\n\n/* Canonical in-memory length unit (Bohr). /\nexport type LengthUnit = \"Bohr\";\n\n/* Units attached to every first-class pseudopotential object. /\nexport interface PseudopotentialUnits {\n energy: EnergyUnit;\n length: LengthUnit;\n}\n\n/* The canonical unit system (Ry / Bohr). /\nexport const CANONICAL_UNITS: PseudopotentialUnits = {\n energy: \"Ry\",\n length: \"Bohr\",\n};\n\n/* Header attributes from PP_HEADER section. /\nexport interface PseudopotentialHeader {\n /* Generation code identifier. /\n generated?: string;\n /* Author of the pseudopotential. /\n author?: string;\n /* Generation date. /\n date?: string;\n /* Brief description. /\n comment?: string;\n /* Chemical element symbol (\"\" when the source format carries none, e.g. raw .cpi). /\n element: string;\n /* Pseudopotential type. /\n pseudoType: PseudopotentialType;\n /* Level of relativistic formalism. /\n relativistic: RelativisticType;\n /* True if ultrasoft (Vanderbilt) pseudopotential. /\n isUltrasoft: boolean;\n /* True if PAW dataset. /\n isPaw: boolean;\n /* True if Coulomb 1/r potential. /\n isCoulomb: boolean;\n /* True if spin-orbit information present. /\n hasSo: boolean;\n /* True if all-electron orbitals present. /\n hasWfc: boolean;\n /* True if GIPAW data present. /\n hasGipaw: boolean;\n /* True if PAW used as GIPAW. /\n pawAsGipaw: boolean;\n /* True if non-linear core correction present. /\n coreCorrection: boolean;\n /* DFT functional identifier. /\n functional: string;\n /* Valence charge. /\n zValence: number;\n /* Total pseudo-valence energy (Ry). /\n totalPsenergy: number;\n /* Suggested wavefunction cutoff (Ry). /\n wfcCutoff: number;\n /* Suggested charge density cutoff (Ry). /\n rhoCutoff: number;\n /* Maximum angular momentum of valence orbitals. /\n lMax: number;\n /* Maximum angular momentum of atomic charge density. /\n lMaxRho: number;\n /* Angular momentum of local channel. /\n lLocal: number;\n /* Number of radial mesh points. /\n meshSize: number;\n /* Number of atomic wavefunctions. /\n numberOfWfc: number;\n /* Number of Kleinman-Bylander projectors. /\n numberOfProj: number;\n /* Numeric XC functional code (PSP8 pspxc). /\n xcCode?: number;\n /* Spin-orbit extension switch (PSP8). /\n extensionSwitch?: number;\n /* Pseudopotential well radius r2well (PSP8/FHI ABINIT header). /\n r2well?: number;\n /* Core charge radius rchrg (PSP8 ABINIT header). /\n rchrg?: number;\n /* Core charge model flag fchrg (PSP8 ABINIT header). /\n fchrg?: number;\n /* Core charge qchrg (PSP8 ABINIT header). /\n qchrg?: number;\n}\n\n/* Radial mesh parameters and data from PP_MESH section. /\nexport interface PseudopotentialMesh {\n /* Grid type discriminator. /\n gridType?: \"logarithmic\" \| \"linear\" \| \"custom\";\n /* Logarithmic grid spacing parameter dx. /\n dx?: number;\n /* Number of mesh points. /\n mesh?: number;\n /* Minimum x value for logarithmic grid. /\n xmin?: number;\n /* Maximum radial coordinate. /\n rmax: number;\n /* Nuclear charge for grid generation. /\n zmesh?: number;\n /* Radial grid points r(i) in Bohr. /\n r: Float64Array;\n /* Radial integration weights rab(i). /\n rab: Float64Array;\n}\n\n/* Local potential from PP_LOCAL section. /\nexport interface PseudopotentialLocal {\n /* Local potential vloc(mesh) in Ry. /\n vloc: Float64Array;\n}\n\n/* A single Kleinman-Bylander projector from PP_BETA section. /\nexport interface BetaProjector {\n /* 1-based position of this projector in the file ordering. /\n index?: number;\n /* Angular momentum of this projector. /\n angularMomentum: number;\n /* Number of mesh points for this projector. /\n cutoffRadiusIndex?: number;\n /* Cutoff radius in Bohr. /\n cutoffRadius?: number;\n /* Norm-conserving radius (US only). /\n normConservingRadius?: number;\n /* Ultrasoft cutoff radius. /\n ultrasoftCutoffRadius: number;\n /* Projector label. /\n label: string;\n /* Projector values beta(r) * r. /\n beta: Float64Array;\n}\n\n/* A single Q_ij^L augmentation function from PP_QIJL.i.j.L (USPP/PAW). /\nexport interface QijlFunction {\n /* First projector index (1-based). /\n i: number;\n /* Second projector index (1-based). /\n j: number;\n /* Augmentation angular momentum. /\n l: number;\n /* Augmentation function values on the radial mesh. /\n qijl: Float64Array;\n}\n\n/* Nonlocal pseudopotential data from PP_NONLOCAL section. /\nexport interface PseudopotentialNonlocal {\n /* Array of beta projectors. /\n betas: BetaProjector[];\n /* D_ij matrix entries. Format: [nb, mb, value in Ry] triples (1-based). /\n dij: Array<[number, number, number]>;\n /* Number of Q function expansion coefficients. /\n nqf?: number;\n /* Augmentation data (USPP/PAW). /\n augmentation?: AugmentationData;\n}\n\n/* Augmentation data from PP_AUGMENTATION section (USPP/PAW). /\nexport interface AugmentationData {\n /* Number of Q function expansion coefficients. /\n nqf?: number;\n /* Number of Q_ij composite functions (nqlc). /\n nqlc?: number;\n /* Augmentation charge shape (BESSEL, GAUSS, PSQ, etc.). /\n shape?: string;\n /* Augmentation matching radius. /\n rMatchAugfun?: number;\n /* Cutoff radius for augmentation (alias: iraug). /\n cutoffR?: number;\n /* Index of radial grid point at the augmentation cutoff radius. /\n cutoffRIndex?: number;\n /* Index of radial grid point at augmentation radius (legacy alias). /\n irc?: number;\n /* Maximum angular momentum of augmentation (accepts l_max_aug / lmax_aug). /\n lmaxAug?: number;\n /* Augmentation pseudization threshold. /\n augmentationEpsilon?: number;\n /* Q_ij norms from PP_Q section. /\n q?: Float64Array;\n /* Electrostatic multipoles from PP_MULTIPOLES section. /\n multipoles?: Float64Array;\n /* Taylor expansion coefficients from PP_QFCOEFF section. /\n qfcoeff?: Float64Array;\n /* Inner radii for Q function from PP_RINNER section. /\n rinner?: Float64Array;\n /* Whether augmentation charge depends on angular momentum. /\n qWithL?: boolean;\n /* Augmentation charge functions from PP_QIJL.i.j.L sections. /\n qijl?: QijlFunction[];\n}\n\n/* Atomic wavefunction from PP_CHI section. /\nexport interface PseudopotentialWfc {\n /* Angular momentum quantum number. /\n l: number;\n /* Occupation number. /\n occupation: number;\n /* Wavefunction label (e.g. \"2S\", \"3P\"). /\n label?: string;\n /* Principal quantum number. /\n n?: number;\n /* Pseudo energy (Ry). /\n pseudoEnergy?: number;\n /* Inner cutoff radius. /\n cutoffRadius?: number;\n /* Ultrasoft cutoff radius. /\n ultrasoftCutoffRadius?: number;\n /* Wavefunction values chi(r) * r. /\n chi: Float64Array;\n}\n\n/* All-electron wavefunction from PP_FULL_WFC section (PAW). /\nexport interface FullWfc {\n /* Angular momentum quantum number. /\n l: number;\n /* Wavefunction label. /\n label: string;\n /* Wavefunction values aewfc(r) * r. /\n aewfc: Float64Array;\n}\n\n/* PAW dataset from PP_PAW section. /\nexport interface PawData {\n /* PAW data format version. /\n pawDataFormat: number;\n /* Core energy constant (Ry). /\n coreEnergy: number;\n /* Occupations of atomic orbitals. /\n occupations: Float64Array;\n /* All-electron core charge. /\n aeNlcc: Float64Array;\n /* All-electron local potential (Ry). /\n aeVloc: Float64Array;\n /* All-electron wavefunctions. /\n aeWfcs: FullWfc[];\n /* Pseudo wavefunctions for each projector. /\n psWfcs: FullWfc[];\n}\n\n/* GIPAW data from PP_GIPAW / PP_GIPAW_RECONSTRUCTION section. /\nexport interface GipawData {\n /* Which tag the data was read from (preserved for round-trip fidelity). /\n tag?: \"PP_GIPAW\" \| \"PP_GIPAW_RECONSTRUCTION\";\n /* GIPAW data format version. /\n gipawDataFormat: number;\n /* Core orbitals. /\n coreOrbitals: Array<{\n n: number;\n l: number;\n orbital: Float64Array;\n }>;\n /* AE and PS orbitals for each valence state. /\n orbitals: Array<{\n l: number;\n label: string;\n aeOrbital: Float64Array;\n psOrbital: Float64Array;\n }>;\n /* AE local potential. /\n vlocAe: Float64Array;\n /* PS local potential. /\n vlocPs: Float64Array;\n}\n\n/* A single relativistic wavefunction entry with its radial data. /\nexport interface RelativisticWfc {\n /* Total angular momentum j of the spinor. /\n jchi: number;\n index?: number;\n els?: string;\n nn?: number;\n lchi?: number;\n oc?: number;\n /* Relativistic wavefunction values (may be absent in legacy files). /\n chi?: Float64Array;\n}\n\n/* A single relativistic projector entry with its radial data. /\nexport interface RelativisticBeta {\n /* Total angular momentum j of the projector. /\n jjj: number;\n index?: number;\n lll?: number;\n /* Relativistic projector values (may be absent in legacy files). /\n beta?: Float64Array;\n}\n\n/* Spin-orbit data from PP_SPIN_ORB section. /\nexport interface SpinOrbitData {\n /* Relativistic wavefunction data. /\n relWfcs: RelativisticWfc[];\n /* Relativistic projector data. /\n relBetas: RelativisticBeta[];\n}\n\n/* GTH/HGH analytical pseudopotential parameters (energies in Ry). /\nexport interface GthData {\n /* Valence electron configuration [s, p, d, ...]. /\n nElec: number[];\n /* Local potential Gaussian radius. /\n rLoc: number;\n /* Local potential Gaussian coefficients (Ry). /\n cexpPpl: number[];\n /* Non-local projector radii per angular momentum channel. /\n rPs: number[];\n /* h-matrix elements [channel][i][j] (Ry). /\n hprj: number[][][];\n /* k-matrix elements for spin-orbit [channel][i][j] (Ry). /\n kprj?: number[][][];\n}\n\n/* Provenance metadata: where this object came from. /\nexport interface Provenance {\n /* Format the data was originally read from. /\n sourceFormat: PseudopotentialFormat;\n /* Generator program name. /\n creator?: string;\n /* Generation date. /\n date?: string;\n /* Embedded input files. /\n inputFiles?: Array<{ name: string; content: string }>;\n /* True when analytical parameters (GTH/HGH) are preserved alongside the grid. /\n analytical?: boolean;\n /* Free-form notes (e.g. appended by resampling operations). /\n notes?: string;\n}\n\n/* Complete pseudopotential data: the first-class pseudopotential object. /\nexport interface Pseudopotential {\n /* Source format this object was parsed from. /\n format: PseudopotentialFormat;\n /* UPF format version (only set for UPF1/UPF2 sources). /\n version?: UPFVersion;\n /* Canonical in-memory units (always Ry / Bohr). /\n units: PseudopotentialUnits;\n /* Provenance metadata (source format, generator, ...). /\n provenance: Provenance;\n /* Human-readable info section. /\n info?: string;\n /* Raw PP_INPUTFILE content, when present in the source. /\n inputFile?: string;\n /* Header with metadata. /\n header: PseudopotentialHeader;\n /* Radial mesh. /\n mesh: PseudopotentialMesh;\n /* Non-linear core correction charge. /\n nlcc?: Float64Array;\n /* Local potential. /\n local: PseudopotentialLocal;\n /* Semilocal potentials (NC only). /\n semilocal?: Array<{\n l: number;\n j?: number;\n vnl: Float64Array;\n }>;\n /* Nonlocal projectors and D_ij. /\n nonlocal: PseudopotentialNonlocal;\n /* Atomic pseudo-wavefunctions. /\n pswfc: PseudopotentialWfc[];\n /* Atomic all-electron wavefunctions (PAW). /\n fullWfc?: FullWfc[];\n /* Atomic charge density. /\n rhoatom: Float64Array;\n /* PAW dataset. /\n paw?: PawData;\n /* GIPAW reconstruction data. /\n gipaw?: GipawData;\n /* Spin-orbit coupling data. /\n spinOrbit?: SpinOrbitData;\n /* GTH/HGH analytical parameters (when format is GTH or HGH). /\n gth?: GthData;\n}\n","/* Parse a Fortran-style number (D-notation) to a JS number. /\nexport function parseFortranNumber(s: string): number {\n return Number.parseFloat(s.replace(/[dD]/g, \"e\"));\n}\n\n/* Parse a Fortran-style boolean string. /\nexport function parseFortranBool(s: string): boolean {\n const v = s.trim().toLowerCase();\n return v === \".true.\" \|\| v === \"true\" \|\| v === \"t\";\n}\n\n/* Parse whitespace-separated text into a Float64Array. /\nexport function parseFloat64Array(text: string): Float64Array {\n const tokens = text.trim().split(/\\s+/).filter(Boolean);\n const arr = new Float64Array(tokens.length);\n for (let i = 0; i < tokens.length; i++) {\n arr[i] = parseFortranNumber(tokens[i]);\n }\n return arr;\n}\n\n/* Parse a string to integer, trimming whitespace. /\nexport function parseIntSafe(s: string): number {\n return Number.parseInt(s.trim(), 10);\n}\n\n/* Format a number in Fortran D-notation. Preserves negative zero. /\nexport function formatFortranNumber(n: number, width = 20): string {\n // 17 significant digits: the minimum that round-trips any double\n // bit-exactly (some generators, e.g. atompaw, write 17 digits).\n const s = n.toExponential(16);\n // toExponential drops the sign of -0; restore it for round-trip fidelity.\n const signed = Object.is(n, -0) && !s.startsWith(\"-\") ? `-${s}` : s;\n const d = signed.replace(/e/, \"D\").replace(/e\\+/, \"D+\").replace(/e-/, \"D-\");\n return d.padStart(width);\n}\n\n/* Format a boolean as Fortran `.true.` / `.false.`. /\nexport function formatFortranBool(b: boolean): string {\n return b ? \".true.\" : \".false.\";\n}\n\n/* Escape special characters for XML attribute values. /\nexport function escapeXmlAttr(s: string): string {\n return s.replace(/&/g, \"&\").replace(/</g, \"<\").replace(/>/g, \">\").replace(/\"/g, \""\");\n}\n\n/* Format a Float64Array as columns of Fortran D-notation numbers. /\nexport function formatDataArray(arr: Float64Array, columns = 4): string {\n const lines: string[] = [];\n for (let i = 0; i < arr.length; i += columns) {\n const row: string[] = [];\n for (let j = 0; j < columns && i + j < arr.length; j++) {\n row.push(formatFortranNumber(arr[i + j]));\n }\n lines.push(row.join(\" \"));\n }\n return lines.join(\"\\n\");\n}\n","module.exports = {}","import { Transform } from 'node:stream';\n\n/\r\n @author: Tobias Nickel\r\n * @created: 06.04.2015\r\n * I needed a small xmlparser that can be used in a worker.\r\n /\r\n\r\n/\r\n Decode XML entities in text and attribute values.\r\n * Unknown or malformed entities are left unchanged.\r\n * @param {string} value\r\n * @returns {string}\r\n /\r\nfunction decodeEntities(value) {\r\n return value.replace(/&(#x[0-9a-fA-F]+\|#\\d+\|amp\|lt\|gt\|quot\|apos);/g, function(match, entity) {\r\n if (entity === 'amp') return '&';\r\n if (entity === 'lt') return '<';\r\n if (entity === 'gt') return '>';\r\n if (entity === 'quot') return '\"';\r\n if (entity === 'apos') return \"'\";\r\n\r\n if (entity[0] === '#') {\r\n var isHex = entity[1] === 'x' \|\| entity[1] === 'X';\r\n var num = parseInt(entity.slice(isHex ? 2 : 1), isHex ? 16 : 10);\r\n if (!Number.isNaN(num) && num >= 0 && num <= 0x10FFFF) {\r\n try {\r\n return String.fromCodePoint(num);\r\n } catch (e) {\r\n return match;\r\n }\r\n }\r\n }\r\n\r\n return match;\r\n });\r\n}\r\n\r\n/\r\n Encode text for safe XML serialization.\r\n * @param {string} value\r\n * @returns {string}\r\n /\r\nfunction encodeTextEntities(value) {\r\n return value\r\n .replace(/&/g, '&')\r\n .replace(/</g, '<')\r\n .replace(/>/g, '>');\r\n}\r\n\r\n/\r\n Encode attribute values for safe XML serialization.\r\n * @param {string} value\r\n * @returns {string}\r\n /\r\nfunction encodeAttributeEntities(value) {\r\n return value\r\n .replace(/&/g, '&')\r\n .replace(/</g, '<')\r\n .replace(/>/g, '>')\r\n .replace(/\"/g, '"')\r\n .replace(/'/g, ''');\r\n}\r\n\r\n/\r\n parseXML / html into a DOM Object. with no validation and some failure tolerance\r\n * @param {string} S your XML to parse\r\n * @param {import('./tXml').ParseOptions} [options] all other options:\r\n * @return {(import('./tXml').TNode \| string)[] \| any}\r\n /\r\nfunction parse(S, options) {\r\n \"txml\";\r\n options = options \|\| {};\r\n\r\n var pos = options.pos \|\| 0;\r\n var keepComments = !!options.keepComments;\r\n var keepWhitespace = options.keepWhitespace !== undefined ? !!options.keepWhitespace : !!options.keepWhitespaces;\r\n var decodeEntitiesEnabled = !!options.decodeEntities;\r\n var skipXmlDeclaration = !!options.skipXmlDeclaration;\r\n\r\n var openBracket = \"<\";\r\n var openBracketCC = \"<\".charCodeAt(0);\r\n var closeBracket = \">\";\r\n var closeBracketCC = \">\".charCodeAt(0);\r\n var minusCC = \"-\".charCodeAt(0);\r\n var slashCC = \"/\".charCodeAt(0);\r\n var questionMarkCC = '?'.charCodeAt(0);\r\n var exclamationCC = '!'.charCodeAt(0);\r\n var singleQuoteCC = \"'\".charCodeAt(0);\r\n var doubleQuoteCC = '\"'.charCodeAt(0);\r\n var equalSignCC = '='.charCodeAt(0);\r\n var openCornerBracketCC = '['.charCodeAt(0);\r\n var closeCornerBracketCC = ']'.charCodeAt(0);\r\n var questionCC = '?'.charCodeAt(0);\r\n\r\n function isXmlDeclarationTag(tagName) {\r\n return typeof tagName === 'string' && tagName.toLowerCase() === '?xml';\r\n }\r\n\r\n\r\n /\r\n parsing a list of entries\r\n * @param {string} tagName\r\n * @returns {(import('./tXml').TNode \| string)[]}\r\n /\r\n function parseChildren(tagName) {\r\n var children = [];\r\n while (S[pos]) {\r\n if (S.charCodeAt(pos) == openBracketCC) {\r\n if (S.charCodeAt(pos + 1) === slashCC) {\r\n var closeStart = pos + 2;\r\n pos = S.indexOf(closeBracket, pos);\r\n\r\n var closeTag = S.substring(closeStart, pos);\r\n if (closeTag.indexOf(tagName) == -1) {\r\n var parsedText = S.substring(0, pos).split('\\n');\r\n throw new Error(\r\n 'Unexpected close tag\\nLine: ' + (parsedText.length - 1) +\r\n '\\nColumn: ' + (parsedText[parsedText.length - 1].length + 1) +\r\n '\\nChar: ' + S[pos]\r\n );\r\n }\r\n\r\n if (pos + 1) pos += 1;\r\n\r\n return children;\r\n } else if (S.charCodeAt(pos + 1) === exclamationCC) {\r\n if (S.charCodeAt(pos + 2) == minusCC) {\r\n //comment support\r\n const startCommentPos = pos;\r\n while (pos !== -1 && !(S.charCodeAt(pos) === closeBracketCC && S.charCodeAt(pos - 1) == minusCC && S.charCodeAt(pos - 2) == minusCC && pos != -1)) {\r\n pos = S.indexOf(closeBracket, pos + 1);\r\n }\r\n if (pos === -1) {\r\n pos = S.length;\r\n }\r\n if (keepComments) {\r\n children.push(S.substring(startCommentPos, pos + 1));\r\n }\r\n } else if (\r\n S.charCodeAt(pos + 2) === openCornerBracketCC &&\r\n S.charCodeAt(pos + 8) === openCornerBracketCC &&\r\n S.substr(pos + 3, 5).toLowerCase() === 'cdata'\r\n ) {\r\n // cdata\r\n var cdataEndIndex = S.indexOf(']]>', pos);\r\n if (cdataEndIndex == -1) {\r\n children.push(S.substr(pos + 9));\r\n pos = S.length;\r\n } else {\r\n children.push(S.substring(pos + 9, cdataEndIndex));\r\n pos = cdataEndIndex + 3;\r\n }\r\n continue;\r\n } else {\r\n // doctypesupport\r\n const startDoctype = pos + 1;\r\n pos += 2;\r\n var encapsuled = false;\r\n while ((S.charCodeAt(pos) !== closeBracketCC \|\| encapsuled === true) && S[pos]) {\r\n if (S.charCodeAt(pos) === openCornerBracketCC) {\r\n encapsuled = true;\r\n } else if (encapsuled === true && S.charCodeAt(pos) === closeCornerBracketCC) {\r\n encapsuled = false;\r\n }\r\n pos++;\r\n }\r\n children.push(S.substring(startDoctype, pos));\r\n }\r\n pos++;\r\n continue;\r\n }\r\n var node = parseNode();\r\n if (skipXmlDeclaration && isXmlDeclarationTag(node.tagName)) {\r\n continue;\r\n }\r\n children.push(node);\r\n } else {\r\n var text = parseText();\r\n if (keepWhitespace) {\r\n if (text.length > 0) {\r\n children.push(text);\r\n }\r\n } else {\r\n var trimmed = text.trim();\r\n if (trimmed.length > 0) {\r\n children.push(trimmed);\r\n }\r\n }\r\n pos++;\r\n }\r\n }\r\n return children;\r\n }\r\n\r\n /\r\n returns the text outside of texts until the first '<'\r\n * @returns {string}\r\n /\r\n function parseText() {\r\n var start = pos;\r\n pos = S.indexOf(openBracket, pos) - 1;\r\n if (pos === -2)\r\n pos = S.length;\r\n var text = S.slice(start, pos + 1);\r\n return decodeEntitiesEnabled ? decodeEntities(text) : text;\r\n }\r\n /\r\n returns text until the first nonAlphabetic letter\r\n * @returns {string}\r\n /\r\n var nameSpacer = '\\r\\n\\t>/= ';\r\n\r\n function parseName() {\r\n var start = pos;\r\n while (nameSpacer.indexOf(S[pos]) === -1 && S[pos]) {\r\n pos++;\r\n }\r\n return S.slice(start, pos);\r\n }\r\n /\r\n is parsing a node, including tagName, Attributes and its children,\r\n * to parse children it uses the parseChildren again, that makes the parsing recursive\r\n * @returns {import('./tXml').TNode}\r\n /\r\n var SelfClosingTags = options.selfClosingTags \|\| options.noChildNodes \|\| ['img', 'br', 'input', 'meta', 'link', 'hr'];\r\n\r\n function parseNode() {\r\n pos++;\r\n const tagName = parseName();\r\n const isProcessingInstruction = tagName[0] === '?';\r\n const instructionContentStart = pos;\r\n /* @type {Record<string, string \| null>} /\r\n const attributes = {};\r\n /* @type {(import('./tXml').TNode \| string)[]} /\r\n let children = [];\r\n\r\n // parsing attributes\r\n while (\r\n S[pos] &&\r\n S.charCodeAt(pos) !== closeBracketCC &&\r\n !(isProcessingInstruction && S.charCodeAt(pos) === questionMarkCC && S.charCodeAt(pos + 1) === closeBracketCC)\r\n ) {\r\n var c = S.charCodeAt(pos);\r\n if ((c > 64 && c < 91) \|\| (c > 96 && c < 123)) {\r\n //if('abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'.indexOf(S[pos])!==-1 ){\r\n var name = parseName();\r\n /* @type {string \| null} /\r\n var value = null;\r\n\r\n // Skip whitespace after the attribute name.\r\n while (S.charCodeAt(pos) === 32 \|\| S.charCodeAt(pos) === 9 \|\| S.charCodeAt(pos) === 10 \|\| S.charCodeAt(pos) === 13) {\r\n pos++;\r\n }\r\n\r\n if (S.charCodeAt(pos) === equalSignCC) {\r\n pos++;\r\n\r\n // Skip whitespace after '='.\r\n while (S.charCodeAt(pos) === 32 \|\| S.charCodeAt(pos) === 9 \|\| S.charCodeAt(pos) === 10 \|\| S.charCodeAt(pos) === 13) {\r\n pos++;\r\n }\r\n\r\n var code = S.charCodeAt(pos);\r\n if (code === singleQuoteCC \|\| code === doubleQuoteCC) {\r\n value = parseString();\r\n if (pos === -1) {\r\n return {\r\n tagName,\r\n attributes,\r\n children,\r\n };\r\n }\r\n } else if (code && code !== closeBracketCC) {\r\n // HTML-style unquoted attribute value: read until whitespace, '/', or '>'.\r\n var valueStart = pos;\r\n while (S[pos] && nameSpacer.indexOf(S[pos]) === -1) {\r\n pos++;\r\n }\r\n value = S.slice(valueStart, pos);\r\n if (decodeEntitiesEnabled) {\r\n value = decodeEntities(value);\r\n }\r\n }\r\n }\r\n attributes[name] = value;\r\n continue;\r\n }\r\n pos++;\r\n }\r\n\r\n const isExplicitSelfClosed = !isProcessingInstruction && S.charCodeAt(pos - 1) === slashCC;\r\n\r\n if (isProcessingInstruction) {\r\n var instructionContent = S.slice(instructionContentStart, pos).trim();\r\n\r\n if (instructionContent.length > 0 && Object.keys(attributes).length === 0) {\r\n children = [instructionContent];\r\n }\r\n\r\n if (S.charCodeAt(pos) === questionMarkCC && S.charCodeAt(pos + 1) === closeBracketCC) {\r\n pos += 2;\r\n } else if (S.charCodeAt(pos) === closeBracketCC) {\r\n pos += 1;\r\n }\r\n\r\n return {\r\n tagName,\r\n attributes,\r\n children,\r\n };\r\n }\r\n\r\n // optional parsing of children\r\n if (S.charCodeAt(pos - 1) !== slashCC && S.charCodeAt(pos - 1) !== questionCC) {\r\n if (tagName == \"script\") {\r\n var start = pos + 1;\r\n pos = S.indexOf('</script>', pos);\r\n children = [S.slice(start, pos)];\r\n pos += 9;\r\n } else if (tagName == \"style\") {\r\n var start = pos + 1;\r\n pos = S.indexOf('</style>', pos);\r\n children = [S.slice(start, pos)];\r\n pos += 8;\r\n } else if (SelfClosingTags.indexOf(tagName) === -1) {\r\n pos++;\r\n children = parseChildren(tagName);\r\n } else {\r\n pos++;\r\n }\r\n } else {\r\n pos++;\r\n }\r\n const node = {\r\n tagName,\r\n attributes,\r\n children,\r\n };\r\n\r\n if (isExplicitSelfClosed) {\r\n Object.defineProperty(node, 'selfClosed', {\r\n value: true,\r\n enumerable: false,\r\n writable: true,\r\n configurable: true,\r\n });\r\n }\r\n\r\n return node;\r\n }\r\n\r\n /\r\n is parsing a string, that starts with a char and with the same usually ' or \"\r\n * @returns {string}\r\n /\r\n\r\n function parseString() {\r\n var startChar = S[pos];\r\n var startpos = pos + 1;\r\n pos = S.indexOf(startChar, startpos);\r\n var value = S.slice(startpos, pos);\r\n return decodeEntitiesEnabled ? decodeEntities(value) : value;\r\n }\r\n\r\n /\r\n Find elements by attribute name and value using regex\r\n * @returns {number}\r\n /\r\n function findElements() {\r\n if (!options \|\| !options.attrName \|\| !options.attrValue) return -1;\r\n var r = new RegExp('\\\\s' + options.attrName + '\\\\s=[\\'\"]' + options.attrValue + '[\\'\"]').exec(S);\r\n if (r) {\r\n return r.index;\r\n } else {\r\n return -1;\r\n }\r\n }\r\n\r\n /** @type {(import('./tXml').TNode \| string)[] \| import('./tXml').TNode} /\r\n var out;\r\n \r\n if (options.attrValue !== undefined) {\r\n options.attrName = options.attrName \|\| 'id';\r\n out = [];\r\n\r\n while ((pos = findElements()) !== -1) {\r\n pos = S.lastIndexOf('<', pos);\r\n if (pos !== -1) {\r\n out.push(parseNode());\r\n }\r\n S = S.substr(pos);\r\n pos = 0;\r\n }\r\n } else if (options.parseNode) {\r\n out = parseNode();\r\n while (skipXmlDeclaration && typeof out === 'object' && out && isXmlDeclarationTag(out.tagName)) {\r\n out = parseNode();\r\n }\r\n } else {\r\n out = parseChildren('');\r\n }\r\n\r\n if (options.filter && Array.isArray(out)) {\r\n out = filter(out, options.filter);\r\n }\r\n\r\n if (options.simplify) {\r\n const arrOut = Array.isArray(out) ? out : [out];\r\n // @ts-ignore - simplify returns different type structure\r\n return simplify(arrOut);\r\n }\r\n\r\n if (options.setPos && typeof out === 'object' && !Array.isArray(out)) {\r\n // @ts-ignore - adding pos property dynamically\r\n out.pos = pos;\r\n }\r\n\r\n // @ts-ignore - return type varies based on options\r\n return out;\r\n}\r\n\r\n/\r\n transform the DomObject to an object that is like the object of PHP`s simple_xml_load_() methods.\r\n this format helps you to write code that is more likely to keep your program working, even if there are small changes in the XML schema.\r\n * be aware, that it is not possible to reproduce the original xml from a simplified version, because the order of elements is not saved.\r\n * therefore your program will be more flexible and easier to read.\r\n \r\n @param {(import('./tXml').TNode \| string)[]} children the childrenList\r\n * @returns {Record<string, any> \| string}\r\n /\r\nfunction simplify(children) {\r\n if (typeof children === 'string') {\r\n return simplify(parse(children));\r\n }\r\n\r\n if (!Array.isArray(children)) {\r\n throw new TypeError('simplify() expects parsed node array or XML string');\r\n }\r\n\r\n /* @type {Record<string, any>} /\r\n var out = {};\r\n \r\n if (!children.length) {\r\n return '';\r\n }\r\n\r\n if (children.length === 1 && typeof children[0] == 'string') {\r\n return children[0];\r\n }\r\n \r\n // map each object\r\n children.forEach(function(child) {\r\n if (typeof child !== 'object') {\r\n return;\r\n }\r\n if (!out[child.tagName])\r\n out[child.tagName] = [];\r\n var kids = simplify(child.children);\r\n out[child.tagName].push(kids);\r\n if (Object.keys(child.attributes).length && typeof kids === 'object' && !Array.isArray(kids)) {\r\n kids._attributes = child.attributes;\r\n }\r\n });\r\n\r\n for (var i in out) {\r\n if (out[i].length == 1) {\r\n out[i] = out[i][0];\r\n }\r\n }\r\n\r\n return out;\r\n}\r\n\r\n\r\n/\r\n similar to simplify, but lost less\r\n \r\n @param {(import('./tXml').TNode \| string)[]} children the childrenList\r\n * @param {Record<string, string \| null>} [parentAttributes]\r\n * @returns {Record<string, any> \| string \| {_attributes: Record<string, string \| null>, value: string}}\r\n /\r\nfunction simplifyLostLess(children, parentAttributes = {}) {\r\n /* @type {Record<string, any>} /\r\n var out = {};\r\n \r\n if (!children.length) {\r\n return out;\r\n }\r\n\r\n if (children.length === 1 && typeof children[0] == 'string') {\r\n return Object.keys(parentAttributes).length ? {\r\n _attributes: parentAttributes,\r\n value: children[0]\r\n } : children[0];\r\n }\r\n \r\n // map each object\r\n children.forEach(function(child) {\r\n if (typeof child !== 'object') {\r\n return;\r\n }\r\n if (!out[child.tagName])\r\n out[child.tagName] = [];\r\n var kids = simplifyLostLess(child.children \|\| [], child.attributes);\r\n out[child.tagName].push(kids);\r\n if (Object.keys(child.attributes).length && typeof kids === 'object' && !Array.isArray(kids)) {\r\n kids._attributes = child.attributes;\r\n }\r\n });\r\n\r\n return out;\r\n}\r\n\r\n/\r\n behaves the same way as Array.filter, if the filter method return true, the element is in the resultList\r\n * @param {(import('./tXml').TNode \| string)[]} children the children of a node\r\n * @param {(node: import('./tXml').TNode, index: number, depth: number, path: string) => boolean} f the filter method\r\n * @param {number} [dept]\r\n * @param {string} [path]\r\n * @returns {import('./tXml').TNode[]}\r\n /\r\nfunction filter(children, f, dept = 0, path = '') {\r\n /* @type {import('./tXml').TNode[]} /\r\n var out = [];\r\n\r\n /\r\n @param {(import('./tXml').TNode \| string)[]} nodes\r\n * @param {number} depth\r\n * @param {string} currentPath\r\n /\r\n function walk(nodes, depth, currentPath) {\r\n nodes.forEach(function(child, i) {\r\n if (typeof child !== 'object') return;\r\n\r\n if (f(child, i, depth, currentPath)) {\r\n out.push(child);\r\n }\r\n\r\n if (child.children) {\r\n walk(child.children, depth + 1, (currentPath ? currentPath + '.' : '') + i + '.' + child.tagName);\r\n }\r\n });\r\n }\r\n\r\n walk(children, dept, path);\r\n return out;\r\n}\r\n\r\n/\r\n stringify a previously parsed string object.\r\n * this is useful,\r\n * 1. to remove whitespace\r\n * 2. to recreate xml data, with some changed data.\r\n * @param {import('./tXml').TNode \| (import('./tXml').TNode \| string)[]} O the object to Stringify\r\n * @param {import('./tXml').StringifyOptions} [options] stringify options\r\n /\r\nfunction stringify(O, options) {\r\n if (!O) return '';\r\n\r\n options = options \|\| {};\r\n var encodeEntitiesEnabled = !!options.encodeEntities;\r\n var keepWhitespace = options.keepWhitespace !== undefined ? !!options.keepWhitespace : !!options.keepWhitespaces;\r\n var selfCloseEmpty = options.selfCloseEmpty !== false;\r\n \r\n var out = '';\r\n\r\n /\r\n @param {(import('./tXml').TNode \| string)[]} nodes\r\n /\r\n function writeChildren(nodes) {\r\n if (nodes) {\r\n for (var i = 0; i < nodes.length; i++) {\r\n var node = nodes[i];\r\n if (typeof node === 'string') {\r\n var textNode = keepWhitespace ? node : node.trim();\r\n out += encodeEntitiesEnabled ? encodeTextEntities(textNode) : textNode;\r\n } else if (node) {\r\n writeNode(node);\r\n }\r\n }\r\n }\r\n }\r\n\r\n /\r\n @param {(import('./tXml').TNode \| string)[] \| undefined} nodes\r\n * @returns {boolean}\r\n /\r\n function hasSerializableChildren(nodes) {\r\n if (!nodes \|\| nodes.length === 0) {\r\n return false;\r\n }\r\n\r\n for (var i = 0; i < nodes.length; i++) {\r\n var child = nodes[i];\r\n if (typeof child === 'string') {\r\n var textNode = keepWhitespace ? child : child.trim();\r\n if (textNode.length > 0) {\r\n return true;\r\n }\r\n } else if (child) {\r\n return true;\r\n }\r\n }\r\n\r\n return false;\r\n }\r\n\r\n /\r\n @param {import('./tXml').TNode} N\r\n /\r\n function writeNode(N) {\r\n if (!N) return;\r\n out += \"<\" + N.tagName;\r\n for (var i in N.attributes) {\r\n var attrValue = N.attributes[i];\r\n if (attrValue === null) {\r\n out += ' ' + i;\r\n } else if (encodeEntitiesEnabled) {\r\n out += ' ' + i + '=\"' + encodeAttributeEntities(attrValue.trim()) + '\"';\r\n } else if (attrValue.indexOf('\"') === -1) {\r\n out += ' ' + i + '=\"' + attrValue.trim() + '\"';\r\n } else {\r\n out += ' ' + i + \"='\" + attrValue.trim() + \"'\";\r\n }\r\n }\r\n if (N.tagName[0] === '?') {\r\n if (N.children && N.children.length) {\r\n var instructionPayload = N.children.filter(function(child) {\r\n return typeof child === 'string';\r\n }).join(' ').trim();\r\n if (instructionPayload.length > 0) {\r\n out += ' ' + instructionPayload;\r\n }\r\n }\r\n out += '?>';\r\n return;\r\n }\r\n\r\n if (N.selfClosed === true) {\r\n out += '/>';\r\n return;\r\n }\r\n\r\n if (selfCloseEmpty && !hasSerializableChildren(N.children)) {\r\n out += '/>';\r\n return;\r\n }\r\n\r\n out += '>';\r\n writeChildren(N.children);\r\n out += '</' + N.tagName + '>';\r\n }\r\n writeChildren(Array.isArray(O) ? O : [O]);\r\n\r\n return out;\r\n}\r\n\r\n\r\n/\r\n use this method to read the text content, of some node.\r\n * It is great if you have mixed content like:\r\n * this text has some <b>big</b> text and a <a href=''>link</a>\r\n * @param {import('./tXml').TNode \| (import('./tXml').TNode \| string)[] \| string} tDom\r\n * @return {string}\r\n /\r\nfunction toContentString(tDom) {\r\n if (Array.isArray(tDom)) {\r\n var out = '';\r\n tDom.forEach(function(e) {\r\n out += ' ' + toContentString(e);\r\n out = out.trim();\r\n });\r\n return out;\r\n } else if (typeof tDom === 'object' && tDom !== null) {\r\n return toContentString(tDom.children)\r\n } else {\r\n return ' ' + tDom;\r\n }\r\n}\r\n\r\n/\r\n @param {string} S\r\n * @param {string} id\r\n * @param {boolean} [simplified]\r\n * @returns {import('./tXml').TNode \| Record<string, any> \| string \| undefined}\r\n /\r\nfunction getElementById(S, id, simplified) {\r\n var out = parse(S, {\r\n attrValue: id\r\n });\r\n return simplified ? simplify(out) : out[0];\r\n}\r\n\r\n/\r\n @param {string} S\r\n * @param {string} classname\r\n * @param {boolean} [simplified]\r\n * @returns {(import('./tXml').TNode \| string)[] \| Record<string, any> \| string}\r\n /\r\nfunction getElementsByClassName(S, classname, simplified) {\r\n const out = parse(S, {\r\n attrName: 'class',\r\n attrValue: '[a-zA-Z0-9- ]' + classname + '[a-zA-Z0-9- ]'\r\n });\r\n return simplified ? simplify(out) : out;\r\n}\r\n\r\n/\r\n Type guard to check if a node is a text node (string).\r\n * Useful for filtering and type narrowing when working with mixed node arrays.\r\n * \r\n * @param {import('./tXml').TNode \| string} node - The node to check\r\n * @returns {node is string} True if the node is a string (text node)\r\n * @example\r\n * const parsed = parse('<div>Hello <span>World</span></div>');\r\n * parsed[0].children.forEach(child => {\r\n * if (isTextNode(child)) {\r\n * console.log('Text:', child);\r\n * }\r\n * });\r\n /\r\nfunction isTextNode(node) {\r\n return typeof node === 'string';\r\n}\r\n\r\n/\r\n Type guard to check if a node is an element node (TNode object).\r\n * Useful for filtering and type narrowing when working with mixed node arrays.\r\n * \r\n * @param {import('./tXml').TNode \| string} node - The node to check\r\n * @returns {node is import('./tXml').TNode} True if the node is a TNode (element node)\r\n * @example\r\n * const parsed = parse('<div>Hello <span>World</span></div>');\r\n * parsed[0].children.forEach(child => {\r\n * if (isElementNode(child)) {\r\n * console.log('Element:', child.tagName);\r\n * }\r\n * });\r\n /\r\nfunction isElementNode(node) {\r\n return typeof node === 'object' && node !== null && 'tagName' in node;\r\n}\n\n// @ts-ignore - node:stream types are available in Node.js 18+\r\n\r\n/\r\n Find the position directly behind the root opening tag.\r\n * Returns -1 when more data is needed.\r\n * @param {string} xml\r\n * @returns {number}\r\n /\r\nfunction detectRootContentOffset(xml) {\r\n let i = 0;\r\n\r\n while (i < xml.length) {\r\n const open = xml.indexOf('<', i);\r\n if (open === -1) return -1;\r\n\r\n if (xml.startsWith('<!--', open)) {\r\n const end = xml.indexOf('-->', open + 4);\r\n if (end === -1) return -1;\r\n i = end + 3;\r\n continue;\r\n }\r\n\r\n if (xml.startsWith('<?', open)) {\r\n const end = xml.indexOf('?>', open + 2);\r\n if (end === -1) return -1;\r\n i = end + 2;\r\n continue;\r\n }\r\n\r\n if (xml.startsWith('<!', open)) {\r\n const end = xml.indexOf('>', open + 2);\r\n if (end === -1) return -1;\r\n i = end + 1;\r\n continue;\r\n }\r\n\r\n if (xml[open + 1] === '/') {\r\n i = open + 2;\r\n continue;\r\n }\r\n\r\n let quote = '';\r\n for (let p = open + 1; p < xml.length; p++) {\r\n const ch = xml[p];\r\n if (quote) {\r\n if (ch === quote) quote = '';\r\n continue;\r\n }\r\n if (ch === '\"' \|\| ch === \"'\") {\r\n quote = ch;\r\n continue;\r\n }\r\n if (ch === '>') {\r\n return p + 1;\r\n }\r\n }\r\n\r\n return -1;\r\n }\r\n\r\n return -1;\r\n}\r\n\r\n/\r\n Create a Node.js Transform stream that parses XML chunks\r\n * @param {number\|string} offset - Starting offset; if omitted, root offset is auto-detected\r\n * @param {import('./tXml.d.ts').ParseOptions} [parseOptions] - Options for the XML parser\r\n * @returns {Transform} Transform stream that emits parsed XML nodes\r\n /\r\nfunction transformStream(offset, parseOptions) {\r\n if (!parseOptions) parseOptions = {};\r\n let autoDetectOffset = typeof offset === 'undefined';\r\n if (typeof offset === 'string') {\r\n offset = offset.length;\r\n }\r\n\r\n let position = offset \|\| 0;\r\n let data = '';\r\n\r\n const stream = new Transform({\r\n objectMode: true,\r\n /\r\n @param {any} chunk\r\n * @param {string} encoding\r\n * @param {Function} callback\r\n /\r\n transform(chunk, encoding, callback) {\r\n data += chunk;\r\n\r\n if (autoDetectOffset) {\r\n const detectedOffset = detectRootContentOffset(data);\r\n if (detectedOffset === -1) {\r\n callback();\r\n return;\r\n }\r\n position = detectedOffset;\r\n autoDetectOffset = false;\r\n }\r\n\r\n let lastPos = 0;\r\n\r\n while (true) {\r\n position = data.indexOf('<', position) + 1;\r\n \r\n if (!position) {\r\n position = lastPos;\r\n callback();\r\n return;\r\n }\r\n\r\n if (data[position] === '/') {\r\n position = position + 1;\r\n lastPos = position;\r\n continue;\r\n }\r\n\r\n if (data[position] === '!' && data[position + 1] === '-' && data[position + 2] === '-') {\r\n const commentEnd = data.indexOf('-->', position + 3);\r\n if (commentEnd === -1) {\r\n data = data.slice(lastPos);\r\n position = 0;\r\n callback();\r\n return;\r\n }\r\n\r\n if (parseOptions.keepComments) {\r\n this.push(data.substring(position - 1, commentEnd + 3));\r\n }\r\n\r\n position = commentEnd + 1;\r\n lastPos = commentEnd;\r\n continue;\r\n }\r\n\r\n const res = parse(data, {\r\n ...parseOptions,\r\n pos: position - 1,\r\n parseNode: true,\r\n setPos: true\r\n });\r\n\r\n // When setPos is true, parse returns an object with pos property\r\n // @ts-ignore - res has pos property when setPos option is true\r\n position = res.pos;\r\n\r\n if (position > (data.length - 1) \|\| position < lastPos) {\r\n data = data.slice(lastPos);\r\n position = 0;\r\n callback();\r\n return;\r\n } else {\r\n this.push(res);\r\n lastPos = position;\r\n }\r\n }\r\n }\r\n });\r\n\r\n return stream;\r\n}\r\n\r\n/\r\n Create a Web Streams API TransformStream that parses XML chunks\r\n * Compatible with browsers, Deno, Bun, and modern Node.js\r\n * @param {number\|string} offset - Starting offset; if omitted, root offset is auto-detected\r\n * @param {import('./tXml.d.ts').ParseOptions} [parseOptions] - Options for the XML parser\r\n * @returns {TransformStream} Web TransformStream that emits parsed XML nodes\r\n /\r\nfunction transformWebStream(offset, parseOptions) {\r\n if (!parseOptions) parseOptions = {};\r\n let autoDetectOffset = typeof offset === 'undefined';\r\n if (typeof offset === 'string') {\r\n offset = offset.length;\r\n }\r\n\r\n let position = offset \|\| 0;\r\n let data = '';\r\n\r\n return new TransformStream({\r\n /\r\n @param {any} chunk\r\n * @param {any} controller\r\n /\r\n transform(chunk, controller) {\r\n data += chunk;\r\n\r\n if (autoDetectOffset) {\r\n const detectedOffset = detectRootContentOffset(data);\r\n if (detectedOffset === -1) {\r\n return;\r\n }\r\n position = detectedOffset;\r\n autoDetectOffset = false;\r\n }\r\n\r\n let lastPos = 0;\r\n\r\n while (true) {\r\n position = data.indexOf('<', position) + 1;\r\n \r\n if (!position) {\r\n position = lastPos;\r\n return;\r\n }\r\n\r\n if (data[position] === '/') {\r\n position = position + 1;\r\n lastPos = position;\r\n continue;\r\n }\r\n\r\n if (data[position] === '!' && data[position + 1] === '-' && data[position + 2] === '-') {\r\n const commentEnd = data.indexOf('-->', position + 3);\r\n if (commentEnd === -1) {\r\n data = data.slice(lastPos);\r\n position = 0;\r\n return;\r\n }\r\n\r\n if (parseOptions.keepComments) {\r\n controller.enqueue(data.substring(position - 1, commentEnd + 3));\r\n }\r\n\r\n position = commentEnd + 1;\r\n lastPos = commentEnd;\r\n continue;\r\n }\r\n\r\n const res = parse(data, {\r\n ...parseOptions,\r\n pos: position - 1,\r\n parseNode: true,\r\n setPos: true\r\n });\r\n\r\n // When setPos is true, parse returns an object with pos property\r\n // @ts-ignore - res has pos property when setPos option is true\r\n position = res.pos;\r\n\r\n if (position > (data.length - 1) \|\| position < lastPos) {\r\n data = data.slice(lastPos);\r\n position = 0;\r\n return;\r\n } else {\r\n controller.enqueue(res);\r\n lastPos = position;\r\n }\r\n }\r\n }\r\n });\r\n}\n\nexport { filter, getElementById, getElementsByClassName, isElementNode, isTextNode, parse, simplify, simplifyLostLess, stringify, toContentString, transformStream, transformWebStream };\n","import { parse as parseTxml } from \"txml\";\n\nimport { parseFortranNumber, parseIntSafe, parseFortranBool } from \"./fortran-helpers\";\n\n/* An XML node: attributes under `@_<name>`, leaf text under `#text`. /\nexport type XmlNode = Record<string, any>;\n\n/* Get an attribute value from an XML node. /\nexport function attr(node: XmlNode \| undefined, name: string): string {\n return node?.[`@_${name}`] ?? \"\";\n}\n\n/* Get an attribute as a Fortran-number. /\nexport function attrNum(node: XmlNode \| undefined, name: string, fallback = 0): number {\n const v = attr(node, name);\n return v ? parseFortranNumber(v) : fallback;\n}\n\n/* Get an attribute as an integer. /\nexport function attrInt(node: XmlNode \| undefined, name: string, fallback = 0): number {\n const v = attr(node, name);\n return v ? parseIntSafe(v) : fallback;\n}\n\n/* Get an attribute as a Fortran boolean. /\nexport function attrBool(node: XmlNode \| undefined, name: string): boolean {\n return parseFortranBool(attr(node, name) \|\| \".false.\");\n}\n\n/* Extract text content from an XML node. /\nexport function textOf(node: XmlNode \| string \| undefined): string {\n if (typeof node === \"string\") return node;\n if (node && \"#text\" in node) return String(node[\"#text\"]);\n return \"\";\n}\n\n/* Normalize a value or array to an array (ensuring T[]). /\nexport function toArray<T>(v: T \| T[] \| undefined \| null): T[] {\n if (Array.isArray(v)) return v;\n if (v == null) return [];\n return [v];\n}\n\n/* Object entries of an XML node, typed for section iteration. /\nexport function entries(node: XmlNode \| undefined): Array<[string, XmlNode]> {\n return Object.entries(node ?? {}) as Array<[string, XmlNode]>;\n}\n\nconst ENTITY_RE = /&(amp\|lt\|gt\|quot\|apos\|#\\d+\|#x[\\da-fA-F]+);/g;\n\n/\n Decode XML entities. txml leaves them raw, so the adapter decodes the\n * predefined set plus decimal/hex character references.\n /\nexport function decodeEntities(s: string): string {\n if (!s.includes(\"&\")) return s;\n return s.replace(ENTITY_RE, (m, body: string) => {\n switch (body) {\n case \"amp\":\n return \"&\";\n case \"lt\":\n return \"<\";\n case \"gt\":\n return \">\";\n case \"quot\":\n return '\"';\n case \"apos\":\n return \"'\";\n default: {\n const hex = body[1] === \"x\" \|\| body[1] === \"X\";\n const code = parseInt(body.slice(hex ? 2 : 1), hex ? 16 : 10);\n return Number.isFinite(code) ? String.fromCodePoint(code) : m;\n }\n }\n });\n}\n\ninterface TxmlNode {\n tagName: string;\n attributes: Record<string, string>;\n children: Array<TxmlNode \| string>;\n}\n\nfunction convertNode(node: TxmlNode, out: XmlNode): void {\n for (const k of Object.keys(node.attributes)) {\n // trimValues equivalent: attribute values are trimmed.\n out[`@_${k}`] = decodeEntities(node.attributes[k]).trim();\n }\n for (const child of node.children) {\n if (typeof child === \"string\") {\n if (child.trim() === \"\") continue;\n const text = decodeEntities(child);\n const prev = out[\"#text\"];\n out[\"#text\"] = prev === undefined ? text : `${prev as string}${text}`;\n continue;\n }\n // Skip processing instructions (e.g. <?xml ...?>).\n if (child.tagName.startsWith(\"?\")) continue;\n appendChild(out, child.tagName, convertElement(child));\n }\n if (typeof out[\"#text\"] === \"string\") out[\"#text\"] = out[\"#text\"].trim();\n}\n\n/\n Convert one element, mirroring fast-xml-parser value collapsing:\n * attribute-less leaves become bare strings (\"\" when empty).\n /\nfunction convertElement(node: TxmlNode): XmlNode \| string {\n const hasAttrs = Object.keys(node.attributes).length > 0;\n if (!hasAttrs) {\n const parts: string[] = [];\n for (const child of node.children) {\n if (typeof child === \"string\") {\n if (child.trim() !== \"\") parts.push(decodeEntities(child));\n } else if (!child.tagName.startsWith(\"?\")) {\n // Has element children: fall through to object form below.\n const out: XmlNode = {};\n convertNode(node, out);\n return out;\n }\n }\n return parts.join(\"\").trim();\n }\n const out: XmlNode = {};\n convertNode(node, out);\n return out;\n}\n\nfunction appendChild(out: XmlNode, tag: string, sub: XmlNode \| string): void {\n const existing = out[tag];\n if (existing === undefined) out[tag] = sub;\n else if (Array.isArray(existing)) existing.push(sub);\n else out[tag] = [existing, sub];\n}\n\n/\n Parse XML text into an XmlNode tree (txml-backed).\n \n Equivalent semantics to the previous fast-xml-parser configuration:\n * attributes under `@_`, leaf text under `#text`, repeated tags as arrays.\n * Singletons stay objects — use toArray() when iterating sections.\n /\nexport function parseXml(text: string): XmlNode {\n const doc: XmlNode = {};\n for (const node of parseTxml(text) as TxmlNode[]) {\n if (typeof node === \"string\") continue;\n if (node.tagName.startsWith(\"?\")) continue;\n appendChild(doc, node.tagName, convertElement(node));\n }\n return doc;\n}\n","import type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n FullWfc,\n AugmentationData,\n PawData,\n GipawData,\n SpinOrbitData,\n RelativisticWfc,\n RelativisticBeta,\n QijlFunction,\n PseudopotentialType,\n RelativisticType,\n UPFVersion,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFortranBool,\n parseFloat64Array,\n parseIntSafe,\n formatFortranNumber,\n formatFortranBool,\n escapeXmlAttr,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n attrBool,\n textOf,\n toArray,\n entries,\n parseXml,\n} from \"./xml-helpers\";\n\nfunction parseData(text: string): Float64Array {\n return parseFloat64Array(text);\n}\n\n/* Parse optional radial data: undefined when the element has no text. /\nfunction parseOptionalData(text: string): Float64Array \| undefined {\n return text.trim() ? parseData(text) : undefined;\n}\n\n// ── Section parsers ────────────────────────────────────────────────\n\nfunction parseHeader(node: XmlNode): PseudopotentialHeader {\n return {\n generated: attr(node, \"generated\") \|\| undefined,\n author: attr(node, \"author\") \|\| undefined,\n date: attr(node, \"date\") \|\| undefined,\n comment: attr(node, \"comment\") \|\| undefined,\n element: attr(node, \"element\").trim(),\n pseudoType: (attr(node, \"pseudo_type\") as PseudopotentialType) \|\| \"NC\",\n relativistic: (attr(node, \"relativistic\") as RelativisticType) \|\| \"scalar\",\n isUltrasoft: attrBool(node, \"is_ultrasoft\"),\n isPaw: attrBool(node, \"is_paw\"),\n isCoulomb: attrBool(node, \"is_coulomb\"),\n hasSo: attrBool(node, \"has_so\"),\n hasWfc: attrBool(node, \"has_wfc\"),\n hasGipaw: attrBool(node, \"has_gipaw\"),\n pawAsGipaw: attrBool(node, \"paw_as_gipaw\"),\n coreCorrection: attrBool(node, \"core_correction\"),\n functional: attr(node, \"functional\"),\n zValence: attrNum(node, \"z_valence\"),\n totalPsenergy: attrNum(node, \"total_psenergy\"),\n wfcCutoff: attrNum(node, \"wfc_cutoff\"),\n rhoCutoff: attrNum(node, \"rho_cutoff\"),\n lMax: attrInt(node, \"l_max\"),\n lMaxRho: attrInt(node, \"l_max_rho\"),\n lLocal: attrInt(node, \"l_local\", -1),\n meshSize: attrInt(node, \"mesh_size\"),\n numberOfWfc: attrInt(node, \"number_of_wfc\"),\n numberOfProj: attrInt(node, \"number_of_proj\"),\n };\n}\n\nfunction parseMesh(node: XmlNode): PseudopotentialMesh {\n const dx = attr(node, \"dx\") ? attrNum(node, \"dx\") : undefined;\n return {\n gridType: dx != null ? \"logarithmic\" : \"custom\",\n dx,\n mesh: attr(node, \"mesh\") ? attrInt(node, \"mesh\") : undefined,\n xmin: attr(node, \"xmin\") ? attrNum(node, \"xmin\") : undefined,\n rmax: attrNum(node, \"rmax\"),\n zmesh: attr(node, \"zmesh\") ? attrNum(node, \"zmesh\") : undefined,\n r: parseData(textOf(node[\"PP_R\"])),\n rab: parseData(textOf(node[\"PP_RAB\"])),\n };\n}\n\nfunction parseLocal(node: XmlNode): PseudopotentialLocal {\n return { vloc: parseData(textOf(node)) };\n}\n\nfunction parseBeta(node: XmlNode): BetaProjector {\n return {\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n angularMomentum: attrInt(node, \"angular_momentum\"),\n cutoffRadiusIndex: attr(node, \"cutoff_radius_index\")\n ? attrInt(node, \"cutoff_radius_index\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n normConservingRadius: attr(node, \"norm_conserving_radius\")\n ? attrNum(node, \"norm_conserving_radius\")\n : undefined,\n ultrasoftCutoffRadius: attrNum(node, \"ultrasoft_cutoff_radius\"),\n label: attr(node, \"label\"),\n beta: parseData(textOf(node)),\n };\n}\n\nfunction parseQijlKey(key: string): { i: number; j: number; l: number } \| null {\n const m = key.match(/^PP_QIJL\\.(\\d+)\\.(\\d+)\\.(\\d+)$/);\n if (!m) return null;\n return { i: parseIntSafe(m[1]), j: parseIntSafe(m[2]), l: parseIntSafe(m[3]) };\n}\n\nfunction parseAugmentation(node: XmlNode): AugmentationData {\n const qijl: QijlFunction[] = [];\n for (const [key, val] of entries(node)) {\n const ids = parseQijlKey(key);\n if (ids) {\n for (const q of toArray(val)) {\n qijl.push({ ...ids, qijl: parseData(textOf(q)) });\n }\n }\n }\n qijl.sort((a, b) => a.i - b.i \|\| a.j - b.j \|\| a.l - b.l);\n\n return {\n nqf: attr(node, \"nqf\") ? attrInt(node, \"nqf\") : undefined,\n nqlc: attr(node, \"nqlc\") ? attrInt(node, \"nqlc\") : undefined,\n qWithL: attr(node, \"q_with_l\") ? attrBool(node, \"q_with_l\") : undefined,\n shape: attr(node, \"shape\") \|\| undefined,\n rMatchAugfun: attr(node, \"r_match_augfun\")\n ? attrNum(node, \"r_match_augfun\")\n : undefined,\n cutoffR: attr(node, \"cutoff_r\")\n ? attrNum(node, \"cutoff_r\")\n : undefined,\n cutoffRIndex: attr(node, \"cutoff_r_index\")\n ? attrInt(node, \"cutoff_r_index\")\n : attr(node, \"iraug\")\n ? attrInt(node, \"iraug\")\n : undefined,\n irc: attr(node, \"irc\") ? attrInt(node, \"irc\") : undefined,\n lmaxAug: attr(node, \"l_max_aug\")\n ? attrInt(node, \"l_max_aug\")\n : attr(node, \"lmax_aug\")\n ? attrInt(node, \"lmax_aug\")\n : undefined,\n augmentationEpsilon: attr(node, \"augmentation_epsilon\")\n ? attrNum(node, \"augmentation_epsilon\")\n : undefined,\n q: node[\"PP_Q\"] ? parseData(textOf(node[\"PP_Q\"])) : undefined,\n multipoles: node[\"PP_MULTIPOLES\"]\n ? parseData(textOf(node[\"PP_MULTIPOLES\"]))\n : undefined,\n qfcoeff: node[\"PP_QFCOEFF\"]\n ? parseData(textOf(node[\"PP_QFCOEFF\"]))\n : undefined,\n rinner: node[\"PP_RINNER\"]\n ? parseData(textOf(node[\"PP_RINNER\"]))\n : undefined,\n qijl: qijl.length > 0 ? qijl : undefined,\n };\n}\n\nfunction parseNonlocal(node: XmlNode): PseudopotentialNonlocal {\n const betas: BetaProjector[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_BETA\" \|\| key.startsWith(\"PP_BETA.\")) {\n betas.push(...toArray(val).map(parseBeta));\n }\n }\n\n const dijText = textOf(node[\"PP_DIJ\"]);\n const tokens = dijText.trim().split(/\\s+/).filter(Boolean).map(parseFortranNumber);\n const dij: Array<[number, number, number]> = [];\n\n if (tokens.length > 0) {\n const nProj = betas.length;\n\n // Triplet format wins when every (nb, mb) pair is a plausible 1-based\n // projector index. This resolves the ambiguity where a triplet file\n // with nProj diagonal entries has exactly nProj^2 tokens (e.g. 3\n // projectors with 3 diagonal triplets = 9 tokens): a flat matrix of\n // floats is essentially never index-clean, while real triplets always\n // are.\n let tripletClean = false;\n if (nProj > 0 && tokens.length % 3 === 0) {\n tripletClean = true;\n for (let k = 0; k < tokens.length; k += 3) {\n const nb = tokens[k];\n const mb = tokens[k + 1];\n if (\n !Number.isInteger(nb) \|\|\n !Number.isInteger(mb) \|\|\n nb < 1 \|\|\n mb < 1 \|\|\n nb > nProj \|\|\n mb > nProj\n ) {\n tripletClean = false;\n break;\n }\n }\n }\n\n if (tripletClean) {\n for (let k = 0; k < tokens.length; k += 3) {\n dij.push([tokens[k], tokens[k + 1], tokens[k + 2]]);\n }\n }\n // Flat matrix format: tokens.length == nProj^2, row-major\n else if (nProj > 0 && tokens.length === nProj nProj) {\n for (let i = 0; i < nProj; i++) {\n for (let j = 0; j < nProj; j++) {\n dij.push([i + 1, j + 1, tokens[i * nProj + j]]);\n }\n }\n }\n // Lenient fallback: token count divisible by 3, parsed as triplets\n // even when the indices look out of range (legacy tolerance).\n else if (tokens.length % 3 === 0) {\n for (let k = 0; k < tokens.length; k += 3) {\n dij.push([tokens[k], tokens[k + 1], tokens[k + 2]]);\n }\n }\n }\n\n // PP_AUGMENTATION (optional, child of PP_NONLOCAL)\n const augmentation = node[\"PP_AUGMENTATION\"]\n ? parseAugmentation(node[\"PP_AUGMENTATION\"])\n : undefined;\n\n // nqf lives on the augmentation block; mirror it for convenience.\n const nqf = augmentation?.nqf ?? undefined;\n\n return { betas, dij, nqf, augmentation };\n}\n\nfunction parsePswfcNode(node: XmlNode): PseudopotentialWfc {\n return {\n l: attrInt(node, \"l\"),\n occupation: attrNum(node, \"occupation\"),\n label: attr(node, \"label\"),\n n: attr(node, \"n\") ? attrInt(node, \"n\") : undefined,\n pseudoEnergy: attr(node, \"pseudo_energy\")\n ? attrNum(node, \"pseudo_energy\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n ultrasoftCutoffRadius: attr(node, \"ultrasoft_cutoff_radius\")\n ? attrNum(node, \"ultrasoft_cutoff_radius\")\n : undefined,\n chi: parseData(textOf(node)),\n };\n}\n\nfunction parseFullWfcNode(node: XmlNode): FullWfc {\n return {\n l: attrInt(node, \"l\"),\n label: attr(node, \"label\"),\n aewfc: parseData(textOf(node)),\n };\n}\n\n/** Parse PP_PAW, including any non-standard PP_AEWFC/PP_PSWFC children. /\nfunction parsePaw(node: XmlNode): PawData {\n const innerAeWfcs: FullWfc[] = [];\n const innerPsWfcs: FullWfc[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_AEWFC\" \|\| key.startsWith(\"PP_AEWFC.\")) {\n for (const wfc of toArray(val)) innerAeWfcs.push(parseFullWfcNode(wfc));\n }\n if (key === \"PP_PSWFC\" \|\| key.startsWith(\"PP_PSWFC.\")) {\n for (const wfc of toArray(val)) innerPsWfcs.push(parseFullWfcNode(wfc));\n }\n }\n return {\n pawDataFormat: attrInt(node, \"paw_data_format\"),\n coreEnergy: attrNum(node, \"core_energy\"),\n occupations: node[\"PP_OCCUPATIONS\"]\n ? parseData(textOf(node[\"PP_OCCUPATIONS\"]))\n : new Float64Array(0),\n aeNlcc: node[\"PP_AE_NLCC\"]\n ? parseData(textOf(node[\"PP_AE_NLCC\"]))\n : new Float64Array(0),\n aeVloc: node[\"PP_AE_VLOC\"]\n ? parseData(textOf(node[\"PP_AE_VLOC\"]))\n : new Float64Array(0),\n aeWfcs: innerAeWfcs,\n psWfcs: innerPsWfcs,\n };\n}\n\nfunction parseGipaw(\n node: XmlNode,\n tag: \"PP_GIPAW\" \| \"PP_GIPAW_RECONSTRUCTION\",\n): GipawData {\n const coreOrbitals: GipawData[\"coreOrbitals\"] = [];\n const coreOrbsSection = node[\"PP_GIPAW_CORE_ORBITALS\"];\n if (coreOrbsSection) {\n for (const [key, val] of entries(coreOrbsSection)) {\n if (key.startsWith(\"PP_GIPAW_CORE_ORBITAL.\")) {\n for (const co of toArray(val)) {\n coreOrbitals.push({\n n: attrInt(co, \"n\"),\n l: attrInt(co, \"l\"),\n orbital: parseData(textOf(co)),\n });\n }\n }\n }\n }\n\n const orbitals: GipawData[\"orbitals\"] = [];\n const orbsSection = node[\"PP_GIPAW_ORBITALS\"];\n if (orbsSection) {\n for (const [key, val] of entries(orbsSection)) {\n if (key.startsWith(\"PP_GIPAW_ORBITAL.\")) {\n for (const orb of toArray(val)) {\n orbitals.push({\n l: attrInt(orb, \"l\"),\n label: attr(orb, \"label\"),\n aeOrbital: orb[\"PP_GIPAW_ORBITAL_AE\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_AE\"]))\n : new Float64Array(0),\n psOrbital: orb[\"PP_GIPAW_ORBITAL_PS\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_PS\"]))\n : new Float64Array(0),\n });\n }\n }\n }\n }\n\n let vlocAe: Float64Array = new Float64Array(0);\n let vlocPs: Float64Array = new Float64Array(0);\n const vlocalSection = node[\"PP_GIPAW_VLOCAL\"];\n if (vlocalSection) {\n vlocAe = vlocalSection[\"GIPAW_VLOCAL_AE\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_AE\"]))\n : vlocAe;\n vlocPs = vlocalSection[\"GIPAW_VLOCAL_PS\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_PS\"]))\n : vlocPs;\n }\n\n return {\n tag,\n gipawDataFormat: attrInt(node, \"gipaw_data_format\"),\n coreOrbitals,\n orbitals,\n vlocAe,\n vlocPs,\n };\n}\n\nfunction parseRelWfc(node: XmlNode): RelativisticWfc {\n return {\n jchi: attrNum(node, \"jchi\"),\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n els: attr(node, \"els\") \|\| undefined,\n nn: attr(node, \"nn\") ? attrInt(node, \"nn\") : undefined,\n lchi: attr(node, \"lchi\") ? attrInt(node, \"lchi\") : undefined,\n oc: attr(node, \"oc\") ? attrNum(node, \"oc\") : undefined,\n chi: parseOptionalData(textOf(node)),\n };\n}\n\nfunction parseRelBeta(node: XmlNode): RelativisticBeta {\n return {\n jjj: attrNum(node, \"jjj\"),\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n lll: attr(node, \"lll\") ? attrInt(node, \"lll\") : undefined,\n beta: parseOptionalData(textOf(node)),\n };\n}\n\nfunction parseSpinOrbit(node: XmlNode): SpinOrbitData {\n const relWfcs: RelativisticWfc[] = [];\n const relBetas: RelativisticBeta[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_RELWFC\" \|\| key.startsWith(\"PP_RELWFC.\")) {\n for (const wfc of toArray(val)) relWfcs.push(parseRelWfc(wfc));\n }\n if (key === \"PP_RELBETA\" \|\| key.startsWith(\"PP_RELBETA.\")) {\n for (const beta of toArray(val)) relBetas.push(parseRelBeta(beta));\n }\n }\n return { relWfcs, relBetas };\n}\n\n/* Extract raw PP_INPUTFILE content (may hold non-XML generator input). /\nfunction extractInputFile(text: string): string \| undefined {\n const m = text.match(/<PP_INPUTFILE>([\\s\\S]?)<\\/PP_INPUTFILE>/);\n if (!m) return undefined;\n const content = m[1].trim();\n return content \|\| undefined;\n}\n\n// ── Main parser ────────────────────────────────────────────────────\n\n/*\n Parse a UPF v2.0.1 pseudopotential string into a first-class\n * Pseudopotential object.\n \n @param text - The complete UPF file content as a string.\n * @returns A parsed Pseudopotential object.\n * @throws If the text is not valid UPF v2.0.1 format.\n /\nexport function fromUPF(text: string): Pseudopotential {\n const doc = parseXml(text);\n\n const upf: XmlNode = doc?.UPF;\n if (!upf) {\n throw new Error(\"Not a UPF file: missing <UPF> root element\");\n }\n\n const version = ((attr(upf, \"version\") \|\| \"2.0.1\") as UPFVersion);\n\n // PP_INFO (optional, plain text)\n const info = upf[\"PP_INFO\"] ? textOf(upf[\"PP_INFO\"]).trim() \|\| undefined : undefined;\n\n // PP_INPUTFILE (optional, raw text — may contain generator input)\n const inputFile = extractInputFile(text);\n\n // PP_HEADER (required, self-closing tag with attributes)\n if (!upf[\"PP_HEADER\"]) {\n throw new Error(\"Missing PP_HEADER section\");\n }\n const header = parseHeader(upf[\"PP_HEADER\"]);\n\n // PP_MESH (required)\n if (!upf[\"PP_MESH\"]) {\n throw new Error(\"Missing PP_MESH section\");\n }\n const mesh = parseMesh(upf[\"PP_MESH\"]);\n\n // PP_NLCC (optional)\n const nlcc = upf[\"PP_NLCC\"] ? parseData(textOf(upf[\"PP_NLCC\"])) : undefined;\n\n // PP_LOCAL (required)\n if (!upf[\"PP_LOCAL\"]) {\n throw new Error(\"Missing PP_LOCAL section\");\n }\n const local = parseLocal(upf[\"PP_LOCAL\"]);\n\n // PP_SEMILOCAL (optional)\n let semilocal: Pseudopotential[\"semilocal\"] \| undefined;\n if (upf[\"PP_SEMILOCAL\"]) {\n semilocal = toArray<XmlNode>(upf[\"PP_SEMILOCAL\"][\"PP_VNL\"]).map((vnl: XmlNode) => ({\n l: attrInt(vnl, \"L\"),\n j: attr(vnl, \"J\") ? attrNum(vnl, \"J\") : undefined,\n vnl: parseData(textOf(vnl)),\n }));\n }\n\n // PP_NONLOCAL (required)\n if (!upf[\"PP_NONLOCAL\"]) {\n throw new Error(\"Missing PP_NONLOCAL section\");\n }\n const nonlocal = parseNonlocal(upf[\"PP_NONLOCAL\"]);\n\n // PP_PSWFC (optional)\n const pswfcRaw = upf[\"PP_PSWFC\"];\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcRaw) {\n for (const [key, val] of entries(pswfcRaw)) {\n if (key === \"PP_CHI\" \|\| key.startsWith(\"PP_CHI.\")) {\n for (const chi of toArray(val)) {\n pswfc.push(parsePswfcNode(chi));\n }\n }\n }\n }\n\n // PP_FULL_WFC (optional, PAW only)\n let fullWfc: FullWfc[] \| undefined;\n if (upf[\"PP_FULL_WFC\"]) {\n const wfcs: FullWfc[] = [];\n for (const [key, val] of entries(upf[\"PP_FULL_WFC\"])) {\n if (key === \"PP_AEWFC\" \|\| key.startsWith(\"PP_AEWFC\")) {\n for (const wfc of toArray(val)) {\n wfcs.push(parseFullWfcNode(wfc));\n }\n }\n }\n fullWfc = wfcs.length > 0 ? wfcs : undefined;\n }\n\n // PP_RHOATOM (required)\n if (!upf[\"PP_RHOATOM\"]) {\n throw new Error(\"Missing PP_RHOATOM section\");\n }\n const rhoatom = parseData(textOf(upf[\"PP_RHOATOM\"]));\n\n // PP_PAW (optional)\n const paw = upf[\"PP_PAW\"] ? parsePaw(upf[\"PP_PAW\"]) : undefined;\n\n // PP_GIPAW (optional — tag may be PP_GIPAW or PP_GIPAW_RECONSTRUCTION)\n const gipaw = upf[\"PP_GIPAW\"]\n ? parseGipaw(upf[\"PP_GIPAW\"], \"PP_GIPAW\")\n : upf[\"PP_GIPAW_RECONSTRUCTION\"]\n ? parseGipaw(upf[\"PP_GIPAW_RECONSTRUCTION\"], \"PP_GIPAW_RECONSTRUCTION\")\n : undefined;\n\n // PP_SPIN_ORB (optional)\n const spinOrbit = upf[\"PP_SPIN_ORB\"]\n ? parseSpinOrbit(upf[\"PP_SPIN_ORB\"])\n : undefined;\n\n // Merge any non-standard inner PAW wavefunctions into the top-level lists\n // (UPF v2.0.1 spec keeps PP_FULL_WFC / PP_PSWFC as siblings of PP_PAW, but\n // some generators nest PP_AEWFC / PP_PSWFC inside PP_PAW).\n if (paw) {\n if (paw.aeWfcs.length > 0) {\n fullWfc = [...(fullWfc ?? []), ...paw.aeWfcs];\n }\n if (paw.psWfcs.length > 0 && pswfc.length === 0) {\n for (const w of paw.psWfcs) {\n pswfc.push({ l: w.l, occupation: 0, label: w.label, chi: w.aewfc });\n }\n }\n paw.aeWfcs = fullWfc ?? [];\n paw.psWfcs =\n paw.psWfcs.length > 0\n ? paw.psWfcs\n : pswfc.map((w) => ({\n l: w.l,\n label: w.label ?? \"\",\n aewfc: w.chi,\n }));\n }\n\n return {\n format: \"UPF2\",\n version,\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"UPF2\" },\n info,\n inputFile,\n header,\n mesh,\n nlcc,\n local,\n semilocal,\n nonlocal,\n pswfc,\n fullWfc,\n rhoatom,\n paw,\n gipaw,\n spinOrbit,\n };\n}\n\n// ── Serializer ─────────────────────────────────────────────────────\n\n/\n Serialize a first-class Pseudopotential object back to UPF v2.0.1 format.\n \n @param pp - The pseudopotential to serialize.\n * @returns The UPF file content as a string.\n /\nexport function toUPF(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n lines.push(`<UPF version=\"${pp.version ?? \"2.0.1\"}\">`);\n lines.push(\"\");\n\n // PP_INFO\n if (pp.info) {\n lines.push(\"<PP_INFO>\");\n lines.push(pp.info);\n lines.push(\"</PP_INFO>\");\n lines.push(\"\");\n }\n\n // PP_HEADER: header fields take precedence; provenance creator/date fill\n // in for objects arriving from formats without header equivalents (PSML,\n // FHI), so generator stamps survive a hub conversion.\n lines.push(\"<PP_HEADER\");\n lines.push(` generated=\"${escapeXmlAttr(pp.header.generated ?? pp.provenance.creator ?? \"\")}\"`);\n lines.push(` author=\"${escapeXmlAttr(pp.header.author ?? \"\")}\"`);\n lines.push(` date=\"${escapeXmlAttr(pp.header.date ?? pp.provenance.date ?? \"\")}\"`);\n lines.push(` comment=\"${escapeXmlAttr(pp.header.comment ?? \"\")}\"`);\n lines.push(` element=\"${pp.header.element}\"`);\n lines.push(` pseudo_type=\"${pp.header.pseudoType}\"`);\n lines.push(` relativistic=\"${pp.header.relativistic}\"`);\n lines.push(` is_ultrasoft=\"${formatFortranBool(pp.header.isUltrasoft)}\"`);\n lines.push(` is_paw=\"${formatFortranBool(pp.header.isPaw)}\"`);\n lines.push(` is_coulomb=\"${formatFortranBool(pp.header.isCoulomb)}\"`);\n lines.push(` has_so=\"${formatFortranBool(pp.header.hasSo)}\"`);\n lines.push(` has_wfc=\"${formatFortranBool(pp.header.hasWfc)}\"`);\n lines.push(` has_gipaw=\"${formatFortranBool(pp.header.hasGipaw)}\"`);\n lines.push(` paw_as_gipaw=\"${formatFortranBool(pp.header.pawAsGipaw)}\"`);\n lines.push(` core_correction=\"${formatFortranBool(pp.header.coreCorrection)}\"`);\n lines.push(` functional=\"${pp.header.functional}\"`);\n lines.push(` z_valence=\"${formatFortranNumber(pp.header.zValence)}\"`);\n lines.push(` total_psenergy=\"${formatFortranNumber(pp.header.totalPsenergy)}\"`);\n lines.push(` wfc_cutoff=\"${formatFortranNumber(pp.header.wfcCutoff)}\"`);\n lines.push(` rho_cutoff=\"${formatFortranNumber(pp.header.rhoCutoff)}\"`);\n lines.push(` l_max=\"${pp.header.lMax}\"`);\n lines.push(` l_max_rho=\"${pp.header.lMaxRho}\"`);\n lines.push(` l_local=\"${pp.header.lLocal}\"`);\n lines.push(` mesh_size=\"${pp.header.meshSize}\"`);\n lines.push(` number_of_wfc=\"${pp.header.numberOfWfc}\"`);\n lines.push(` number_of_proj=\"${pp.header.numberOfProj}\"/>`);\n lines.push(\"\");\n\n // PP_MESH\n const meshAttrs: string[] = [];\n if (pp.mesh.dx != null) meshAttrs.push(`dx=\"${pp.mesh.dx}\"`);\n if (pp.mesh.mesh != null) meshAttrs.push(`mesh=\"${pp.mesh.mesh}\"`);\n if (pp.mesh.xmin != null) meshAttrs.push(`xmin=\"${pp.mesh.xmin}\"`);\n meshAttrs.push(`rmax=\"${pp.mesh.rmax}\"`);\n if (pp.mesh.zmesh != null) meshAttrs.push(`zmesh=\"${pp.mesh.zmesh}\"`);\n lines.push(`<PP_MESH ${meshAttrs.join(\" \")}>`);\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n lines.push(\"\");\n\n // PP_NLCC (optional)\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n lines.push(\"\");\n }\n\n // PP_LOCAL\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n lines.push(\"\");\n\n // PP_SEMILOCAL (optional)\n if (pp.semilocal) {\n lines.push(\"<PP_SEMILOCAL>\");\n for (const vnl of pp.semilocal) {\n lines.push(`<PP_VNL L=\"${vnl.l}\"${vnl.j !== undefined ? ` J=\"${vnl.j}\"` : \"\"}>`);\n lines.push(formatDataArray(vnl.vnl));\n lines.push(\"</PP_VNL>\");\n }\n lines.push(\"</PP_SEMILOCAL>\");\n lines.push(\"\");\n }\n\n // PP_NONLOCAL\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n const betaAttrs = [\n `angular_momentum=\"${beta.angularMomentum}\"`,\n `label=\"${beta.label}\"`,\n ];\n // Preserve document order without inventing attributes: only write\n // index when the source carried one.\n if (beta.index != null) betaAttrs.unshift(`index=\"${beta.index}\"`);\n if (beta.cutoffRadiusIndex != null) betaAttrs.push(`cutoff_radius_index=\"${beta.cutoffRadiusIndex}\"`);\n if (beta.cutoffRadius != null) betaAttrs.push(`cutoff_radius=\"${formatFortranNumber(beta.cutoffRadius)}\"`);\n if (beta.normConservingRadius != null) betaAttrs.push(`norm_conserving_radius=\"${formatFortranNumber(beta.normConservingRadius)}\"`);\n betaAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(beta.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_BETA ${betaAttrs.join(\" \")}>`);\n lines.push(formatDataArray(beta.beta));\n lines.push(\"</PP_BETA>\");\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(`${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n\n // PP_AUGMENTATION (optional, USPP/PAW)\n if (pp.nonlocal.augmentation) {\n const aug = pp.nonlocal.augmentation;\n const augAttrs: string[] = [];\n if (aug.qWithL != null) augAttrs.push(`q_with_l=\"${aug.qWithL ? \"T\" : \"F\"}\"`);\n if (aug.nqf != null) augAttrs.push(`nqf=\"${aug.nqf}\"`);\n if (aug.nqlc != null) augAttrs.push(`nqlc=\"${aug.nqlc}\"`);\n if (aug.shape != null) augAttrs.push(`shape=\"${aug.shape}\"`);\n if (aug.rMatchAugfun != null) augAttrs.push(`r_match_augfun=\"${formatFortranNumber(aug.rMatchAugfun)}\"`);\n if (aug.cutoffR != null) augAttrs.push(`cutoff_r=\"${formatFortranNumber(aug.cutoffR)}\"`);\n if (aug.cutoffRIndex != null) augAttrs.push(`cutoff_r_index=\"${aug.cutoffRIndex}\"`);\n if (aug.irc != null) augAttrs.push(`irc=\"${aug.irc}\"`);\n if (aug.lmaxAug != null) augAttrs.push(`l_max_aug=\"${aug.lmaxAug}\"`);\n if (aug.augmentationEpsilon != null) augAttrs.push(`augmentation_epsilon=\"${formatFortranNumber(aug.augmentationEpsilon)}\"`);\n lines.push(`<PP_AUGMENTATION ${augAttrs.join(\" \")}>`);\n if (aug.q) {\n lines.push(\"<PP_Q>\");\n lines.push(formatDataArray(aug.q));\n lines.push(\"</PP_Q>\");\n }\n if (aug.multipoles) {\n lines.push(\"<PP_MULTIPOLES>\");\n lines.push(formatDataArray(aug.multipoles));\n lines.push(\"</PP_MULTIPOLES>\");\n }\n if (aug.qfcoeff) {\n lines.push(\"<PP_QFCOEFF>\");\n lines.push(formatDataArray(aug.qfcoeff));\n lines.push(\"</PP_QFCOEFF>\");\n }\n if (aug.rinner) {\n lines.push(\"<PP_RINNER>\");\n lines.push(formatDataArray(aug.rinner));\n lines.push(\"</PP_RINNER>\");\n }\n if (aug.qijl) {\n for (const q of aug.qijl) {\n lines.push(`<PP_QIJL.${q.i}.${q.j}.${q.l}>`);\n lines.push(formatDataArray(q.qijl));\n lines.push(`</PP_QIJL.${q.i}.${q.j}.${q.l}>`);\n }\n }\n lines.push(\"</PP_AUGMENTATION>\");\n }\n\n lines.push(\"</PP_NONLOCAL>\");\n lines.push(\"\");\n\n // PP_PSWFC\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (let i = 0; i < pp.pswfc.length; i++) {\n const wfc = pp.pswfc[i];\n const chiAttrs = [\n `index=\"${i + 1}\"`,\n `l=\"${wfc.l}\"`,\n `occupation=\"${formatFortranNumber(wfc.occupation)}\"`,\n `label=\"${wfc.label ?? \"\"}\"`,\n ];\n if (wfc.n != null) chiAttrs.push(`n=\"${wfc.n}\"`);\n if (wfc.pseudoEnergy != null) chiAttrs.push(`pseudo_energy=\"${formatFortranNumber(wfc.pseudoEnergy)}\"`);\n if (wfc.cutoffRadius != null) chiAttrs.push(`cutoff_radius=\"${formatFortranNumber(wfc.cutoffRadius)}\"`);\n if (wfc.ultrasoftCutoffRadius != null) chiAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(wfc.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_CHI ${chiAttrs.join(\" \")}>`);\n lines.push(formatDataArray(wfc.chi));\n lines.push(\"</PP_CHI>\");\n }\n lines.push(\"</PP_PSWFC>\");\n lines.push(\"\");\n }\n\n // PP_FULL_WFC (optional)\n if (pp.fullWfc && pp.fullWfc.length > 0) {\n lines.push(\"<PP_FULL_WFC>\");\n for (const wfc of pp.fullWfc) {\n lines.push(`<PP_AEWFC l=\"${wfc.l}\" label=\"${wfc.label}\">`);\n lines.push(formatDataArray(wfc.aewfc));\n lines.push(\"</PP_AEWFC>\");\n }\n lines.push(\"</PP_FULL_WFC>\");\n lines.push(\"\");\n }\n\n // PP_RHOATOM\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n lines.push(\"\");\n\n // PP_PAW (optional): block holds OCCUPATIONS / AE_NLCC / AE_VLOC only;\n // wavefunctions live in the top-level PP_PSWFC / PP_FULL_WFC sections.\n if (pp.paw) {\n lines.push(`<PP_PAW paw_data_format=\"${pp.paw.pawDataFormat}\" core_energy=\"${formatFortranNumber(pp.paw.coreEnergy)}\">`);\n if (pp.paw.occupations.length > 0) {\n lines.push(\"<PP_OCCUPATIONS>\");\n lines.push(formatDataArray(pp.paw.occupations));\n lines.push(\"</PP_OCCUPATIONS>\");\n }\n if (pp.paw.aeNlcc.length > 0) {\n lines.push(\"<PP_AE_NLCC>\");\n lines.push(formatDataArray(pp.paw.aeNlcc));\n lines.push(\"</PP_AE_NLCC>\");\n }\n if (pp.paw.aeVloc.length > 0) {\n lines.push(\"<PP_AE_VLOC>\");\n lines.push(formatDataArray(pp.paw.aeVloc));\n lines.push(\"</PP_AE_VLOC>\");\n }\n lines.push(\"</PP_PAW>\");\n lines.push(\"\");\n }\n\n // PP_GIPAW (optional): preserve the original tag variant.\n if (pp.gipaw) {\n const tag = pp.gipaw.tag ?? \"PP_GIPAW\";\n lines.push(`<${tag} gipaw_data_format=\"${pp.gipaw.gipawDataFormat}\">`);\n if (pp.gipaw.coreOrbitals.length > 0) {\n lines.push(`<PP_GIPAW_CORE_ORBITALS number_of_core_orbitals=\"${pp.gipaw.coreOrbitals.length}\">`);\n for (let i = 0; i < pp.gipaw.coreOrbitals.length; i++) {\n const co = pp.gipaw.coreOrbitals[i];\n lines.push(`<PP_GIPAW_CORE_ORBITAL.${i + 1} n=\"${co.n}\" l=\"${co.l}\">`);\n if (co.orbital.length > 0) lines.push(formatDataArray(co.orbital));\n lines.push(`</PP_GIPAW_CORE_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_CORE_ORBITALS>\");\n }\n if (pp.gipaw.orbitals.length > 0) {\n lines.push(\"<PP_GIPAW_ORBITALS>\");\n for (let i = 0; i < pp.gipaw.orbitals.length; i++) {\n const orb = pp.gipaw.orbitals[i];\n lines.push(`<PP_GIPAW_ORBITAL.${i + 1} l=\"${orb.l}\" label=\"${escapeXmlAttr(orb.label)}\">`);\n lines.push(\"<PP_GIPAW_ORBITAL_AE>\");\n lines.push(formatDataArray(orb.aeOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_AE>\");\n lines.push(\"<PP_GIPAW_ORBITAL_PS>\");\n lines.push(formatDataArray(orb.psOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_PS>\");\n lines.push(`</PP_GIPAW_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_ORBITALS>\");\n }\n if (pp.gipaw.vlocAe.length > 0 \|\| pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<PP_GIPAW_VLOCAL>\");\n if (pp.gipaw.vlocAe.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_AE>\");\n lines.push(formatDataArray(pp.gipaw.vlocAe));\n lines.push(\"</GIPAW_VLOCAL_AE>\");\n }\n if (pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_PS>\");\n lines.push(formatDataArray(pp.gipaw.vlocPs));\n lines.push(\"</GIPAW_VLOCAL_PS>\");\n }\n lines.push(\"</PP_GIPAW_VLOCAL>\");\n }\n lines.push(`</${tag}>`);\n lines.push(\"\");\n }\n\n // PP_SPIN_ORB (optional)\n if (pp.spinOrbit) {\n lines.push(\"<PP_SPIN_ORB>\");\n let relIdx = 1;\n for (const wfc of pp.spinOrbit.relWfcs) {\n const attrs = [\n `index=\"${wfc.index ?? relIdx}\"`,\n `jchi=\"${formatFortranNumber(wfc.jchi)}\"`,\n ];\n if (wfc.els != null) attrs.push(`els=\"${escapeXmlAttr(wfc.els)}\"`);\n if (wfc.nn != null) attrs.push(`nn=\"${wfc.nn}\"`);\n if (wfc.lchi != null) attrs.push(`lchi=\"${wfc.lchi}\"`);\n if (wfc.oc != null) attrs.push(`oc=\"${formatFortranNumber(wfc.oc)}\"`);\n lines.push(`<PP_RELWFC ${attrs.join(\" \")}>`);\n if (wfc.chi && wfc.chi.length > 0) lines.push(formatDataArray(wfc.chi));\n lines.push(\"</PP_RELWFC>\");\n relIdx++;\n }\n let betaIdx = 1;\n for (const beta of pp.spinOrbit.relBetas) {\n const attrs = [\n `index=\"${beta.index ?? betaIdx}\"`,\n `jjj=\"${formatFortranNumber(beta.jjj)}\"`,\n ];\n if (beta.lll != null) attrs.push(`lll=\"${beta.lll}\"`);\n lines.push(`<PP_RELBETA ${attrs.join(\" \")}>`);\n if (beta.beta && beta.beta.length > 0) lines.push(formatDataArray(beta.beta));\n lines.push(\"</PP_RELBETA>\");\n betaIdx++;\n }\n lines.push(\"</PP_SPIN_ORB>\");\n lines.push(\"\");\n }\n\n // PP_INPUTFILE (optional, verbatim)\n if (pp.inputFile) {\n lines.push(\"<PP_INPUTFILE>\");\n lines.push(pp.inputFile);\n lines.push(\"</PP_INPUTFILE>\");\n lines.push(\"\");\n }\n\n lines.push(\"</UPF>\");\n\n return lines.join(\"\\n\");\n}\n","/\n UPF v1 pseudopotential parser and serializer.\n \n UPF v1 is the legacy Quantum ESPRESSO format with fixed-width headers\n * and `<SECTION>`/`</SECTION>` delimiters (not XML attributes).\n * Units: Rydberg (energy), Bohr (length) — same as UPF v2.\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nfunction extractSection(text: string, tag: string): string \| null {\n const open = `<${tag}>`;\n const close = `</${tag}>`;\n const start = text.indexOf(open);\n if (start === -1) return null;\n const end = text.indexOf(close, start);\n if (end === -1) return null;\n return text.substring(start + open.length, end);\n}\n\nfunction extractSubSection(text: string, tag: string): string \| null {\n return extractSection(text, tag);\n}\n\nfunction lines(text: string): string[] {\n return text.split(\"\\n\").filter((l) => l.trim().length > 0);\n}\n\n/\n Parse a UPF v1 pseudopotential string.\n \n UPF v1 format:\n * - First line: version number (0 or 1)\n * - Header: element, type, functional, z_valence, etc.\n * - `<PP_MESH>`: radial grid\n * - `<PP_LOCAL>`: local potential\n * - `<PP_NONLOCAL>`: projectors and D_ij\n * - `<PP_PSWFC>`: pseudo wavefunctions\n * - `<PP_RHOATOM>`: atomic charge density\n /\nexport function fromUPFv1(text: string): Pseudopotential {\n // Detect UPF v1: first non-empty line should be a number\n const firstLine = text.trim().split(\"\\n\")[0].trim();\n const versionMatch = firstLine.match(/^(\\d+)/);\n if (!versionMatch) {\n throw new Error(\"Not a UPF v1 file: first line is not a version number\");\n }\n\n // Extract header section\n const headerSection = extractSection(text, \"PP_HEADER\");\n if (!headerSection) throw new Error(\"Missing PP_HEADER section\");\n\n const headerLines = lines(headerSection);\n\n // Parse header fields (UPF v1 uses free-format Fortran reads)\n // Line format varies; we parse what we can find\n let element = \"X\";\n let pseudoType: PseudopotentialHeader[\"pseudoType\"] = \"NC\";\n let functional = \"\";\n let zValence = 0;\n let lMax = 0;\n let meshSize = 0;\n let numberOfWfc = 0;\n let numberOfProj = 0;\n let coreCorrection = false;\n\n for (const line of headerLines) {\n const trimmed = line.trim();\n // Try to extract element from first meaningful line\n // Handle quoted element names like 'H' or unquoted like H\n const elemMatch = trimmed.match(/^['\"]?([A-Z][a-z]?)['\"]?(?:\\s\|$)/);\n if (elemMatch) {\n element = elemMatch[1];\n }\n // Look for pseudo type indicators\n if (trimmed.includes(\"'NC'\") \|\| trimmed.includes('\"NC\"') \|\| trimmed.includes(\"NC\")) {\n pseudoType = \"NC\";\n }\n if (trimmed.includes(\"'US'\") \|\| trimmed.includes('\"US\"') \|\| trimmed.includes(\"US\")) {\n pseudoType = \"US\";\n }\n if (trimmed.includes(\"'PAW'\") \|\| trimmed.includes('\"PAW\"') \|\| trimmed.includes(\"PAW\")) {\n pseudoType = \"PAW\";\n }\n // Look for functional (quoted string like 'SLA-PW-PBE-PBE')\n const funcMatch = trimmed.match(/^['\"]([^'\"]+)['\"]/);\n if (funcMatch && (funcMatch[1].includes(\"SLA\") \|\| funcMatch[1].includes(\"PBE\") \|\| funcMatch[1].includes(\"LDA\"))) {\n functional = funcMatch[1];\n }\n // Look for z_valence\n const zMatch = trimmed.match(/(\\d+\\.?\\d)\\s(?:zp\|z_valence\|z_p)/i);\n if (zMatch) zValence = parseFloat(zMatch[1]);\n // Look for lmax\n const lmaxMatch = trimmed.match(/lmax\\s=\\s(\\d+)/i);\n if (lmaxMatch) lMax = parseInt(lmaxMatch[1]);\n // Look for mesh size\n const meshMatch = trimmed.match(/mesh\\s=\\s(\\d+)/i);\n if (meshMatch) meshSize = parseInt(meshMatch[1]);\n // Look for number of wavefunctions and projectors\n const nwfcMatch = trimmed.match(/(\\d+)\\s+(\\d+)\\s+(?:nwfc\|nbeta)/i);\n if (nwfcMatch) {\n numberOfWfc = parseInt(nwfcMatch[1]);\n numberOfProj = parseInt(nwfcMatch[2]);\n }\n // Core correction\n if (trimmed.includes(\".true.\") \|\| trimmed.includes(\"T\")) {\n coreCorrection = true;\n }\n }\n\n // Parse PP_MESH section\n const meshSection = extractSection(text, \"PP_MESH\");\n let r: Float64Array = new Float64Array(0);\n let rab: Float64Array = new Float64Array(0);\n\n if (meshSection) {\n const rSection = extractSubSection(meshSection, \"PP_R\");\n const rabSection = extractSubSection(meshSection, \"PP_RAB\");\n if (rSection) r = parseFloat64Array(rSection);\n if (rabSection) rab = parseFloat64Array(rabSection);\n }\n\n if (r.length === 0) throw new Error(\"Empty or missing PP_R section\");\n meshSize = r.length;\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Parse PP_LOCAL section\n const localSection = extractSection(text, \"PP_LOCAL\");\n if (!localSection) throw new Error(\"Missing PP_LOCAL section\");\n const local: PseudopotentialLocal = { vloc: parseFloat64Array(localSection) };\n\n // Parse PP_NONLOCAL section\n const nonlocalSection = extractSection(text, \"PP_NONLOCAL\");\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n\n if (nonlocalSection) {\n // Parse beta projectors\n const betaMatches = nonlocalSection.match(/<PP_BETA[^>]>([\\s\\S]?)<\\/PP_BETA>/g);\n if (betaMatches) {\n for (const betaBlock of betaMatches) {\n const inner = betaBlock.replace(/<\\/?PP_BETA[^>]>/g, \"\");\n const innerLines = lines(inner);\n if (innerLines.length >= 2) {\n // First line: nbeta, lll, label\n const metaParts = innerLines[0].trim().split(/\\s+/);\n const l = metaParts.length >= 2 ? parseInt(metaParts[1]) : 0;\n const label = metaParts.length >= 3 ? metaParts[2].replace(/['\"]/g, \"\") : `l=${l}`;\n\n // Second line: kkbeta (cutoff index)\n const cutoffLine = innerLines[1].trim().split(/\\s+/);\n const cutoffIndex = cutoffLine.length >= 1 ? parseInt(cutoffLine[0]) : 0;\n\n // Remaining lines: projector data\n const dataText = innerLines.slice(1).join(\"\\n\");\n const betaData = parseFloat64Array(dataText.replace(/^\\s\\d+\\s+/gm, \"\"));\n\n betas.push({\n angularMomentum: l,\n cutoffRadiusIndex: cutoffIndex,\n ultrasoftCutoffRadius: 0,\n label,\n beta: betaData,\n });\n }\n }\n }\n\n // Parse D_ij\n const dijSection = extractSection(nonlocalSection, \"PP_DIJ\");\n if (dijSection) {\n const dijLines = lines(dijSection);\n for (const line of dijLines) {\n const parts = line.trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 3) {\n const nb = parseInt(parts[0]);\n const mb = parseInt(parts[1]);\n const val = parseFortranNumber(parts[2]);\n if (!isNaN(nb) && !isNaN(mb) && !isNaN(val)) {\n dij.push([nb, mb, val]);\n }\n }\n }\n }\n }\n\n const nonlocal: PseudopotentialNonlocal = { betas, dij };\n\n // Parse PP_PSWFC section\n const pswfcSection = extractSection(text, \"PP_PSWFC\");\n const pswfc: PseudopotentialWfc[] = [];\n\n if (pswfcSection) {\n const pswfcLines = lines(pswfcSection);\n let i = 0;\n while (i < pswfcLines.length) {\n const line = pswfcLines[i].trim();\n // Wavefunction header: label l oc\n const wfcMatch = line.match(/['\"]?(\\w+)['\"]?\\s+(\\d+)\\s+([\\d.]+)/);\n if (wfcMatch) {\n const label = wfcMatch[1];\n const l = parseInt(wfcMatch[2]);\n const occupation = parseFloat(wfcMatch[3]);\n i++;\n // Collect data lines until next header or end\n const dataLines: string[] = [];\n while (i < pswfcLines.length && !pswfcLines[i].trim().match(/['\"]?\\w+['\"]?\\s+\\d+\\s+[\\d.]+/)) {\n dataLines.push(pswfcLines[i]);\n i++;\n }\n const chi = parseFloat64Array(dataLines.join(\"\\n\"));\n pswfc.push({ l, occupation, label, chi });\n } else {\n i++;\n }\n }\n }\n\n // Parse PP_NLCC section (optional)\n const nlccSection = extractSection(text, \"PP_NLCC\");\n const nlcc = nlccSection ? parseFloat64Array(nlccSection) : undefined;\n\n // Parse PP_RHOATOM section\n const rhoatomSection = extractSection(text, \"PP_RHOATOM\");\n const rhoatom = rhoatomSection ? parseFloat64Array(rhoatomSection) : new Float64Array(meshSize);\n\n return {\n format: \"UPF1\",\n version: \"1.0.0\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"UPF1\" },\n header: {\n element,\n pseudoType,\n relativistic: \"scalar\",\n isUltrasoft: pseudoType === \"US\",\n isPaw: pseudoType === \"PAW\",\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize,\n numberOfWfc,\n numberOfProj,\n },\n mesh,\n nlcc,\n local,\n nonlocal,\n pswfc,\n rhoatom,\n };\n}\n\n/\n Serialize a Pseudopotential to UPF v1 format.\n \n NOTE: UPF v1 is a legacy format. This serializer produces valid UPF v1\n * but UPF v2 is preferred for new files.\n /\nexport function toUPFv1(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n // Version line\n lines.push(\" 0\");\n lines.push(\"<PP_HEADER>\");\n lines.push(` '${pp.header.element}'`);\n lines.push(` '${pp.header.pseudoType}'`);\n lines.push(` ${pp.header.coreCorrection ? \".true.\" : \".false.\"} nlcc`);\n lines.push(` '${pp.header.functional}' dft`);\n lines.push(` ${pp.header.zValence.toFixed(8)} zp`);\n lines.push(` ${pp.header.totalPsenergy.toFixed(8)} etotps`);\n lines.push(` ${pp.header.wfcCutoff.toFixed(2)} ${pp.header.rhoCutoff.toFixed(2)} ecutwfc,ecutrho`);\n lines.push(` ${pp.header.lMax} 'lmax'`);\n lines.push(` ${pp.mesh.r.length} 'mesh'`);\n lines.push(` ${pp.pswfc.length} ${pp.nonlocal.betas.length} 'nwfc nbeta'`);\n\n // Wavefunction labels\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(4)}`);\n }\n\n lines.push(\"</PP_HEADER>\");\n\n lines.push(\"<PP_MESH>\");\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n }\n\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n lines.push(`<PP_BETA>`);\n lines.push(` ${i + 1} ${beta.angularMomentum} '${beta.label}'`);\n lines.push(` ${pp.mesh.r.length}`);\n lines.push(formatDataArray(beta.beta));\n lines.push(`</PP_BETA>`);\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(` ${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n lines.push(\"</PP_NONLOCAL>\");\n\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(8)}`);\n lines.push(formatDataArray(wfc.chi));\n }\n lines.push(\"</PP_PSWFC>\");\n }\n\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n\n return lines.join(\"\\n\");\n}\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported energy unit identifiers. /\nexport type EnergyUnits = \"eV\" \| \"Hartree\" \| \"Rydberg\" \| \"kJ/mol\" \| \"kcal/mol\";\n\nconst EnergyConversions: Record<EnergyUnits, number> = {\n eV: 1,\n Hartree: 27.2114,\n Rydberg: 13.6057,\n \"kJ/mol\": 0.0103643,\n \"kcal/mol\": 0.0433641,\n};\n\nconst EnergyAliases: Record<string, EnergyUnits> = {\n Ha: \"Hartree\",\n Ry: \"Rydberg\",\n ev: \"eV\",\n electronvolt: \"eV\",\n};\n\n/* Unit system for energy conversions with eV as base. /\nexport const EnergyUnitSystem = {\n conversions: EnergyConversions,\n aliases: EnergyAliases,\n\n convert(value: number, from: EnergyUnits \| string, to: EnergyUnits \| string) {\n return convertMeasurement(\n value,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: EnergyUnits \| string,\n to: EnergyUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n};\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported angle unit identifiers. /\nexport type AngleUnits = \"rad\" \| \"deg\" \| \"grad\";\n\nconst AngleConversions: Record<AngleUnits, number> = {\n rad: 1,\n deg: Math.PI / 180,\n grad: Math.PI / 200,\n};\n\nconst AngleAliases: Record<string, AngleUnits> = {\n \"°\": \"deg\",\n deg: \"deg\",\n rad: \"rad\",\n gon: \"grad\",\n};\n\n/* Unit system for angle conversions with radian as base. /\nexport const AngleUnitSystem = {\n conversions: AngleConversions,\n aliases: AngleAliases,\n\n convert(value: number, from: AngleUnits \| string, to: AngleUnits \| string) {\n return convertMeasurement(\n value,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: AngleUnits \| string,\n to: AngleUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n },\n};\n","/\n Unit conversion helpers for pseudopotentials.\n \n Canonical in-memory units: Rydberg (energy) / Bohr (length) — the\n * UPF-native system. Hartree-based formats (PSP8, FHI/CPI, PSML, GTH) convert\n * on parse and back on serialize. Both factors are exact powers of two, so\n * same-format round-trips stay bit-exact.\n /\n\nimport type { Pseudopotential } from \"./pseudopotential\";\n\nimport { EnergyUnitSystem } from \"../units\";\n\n/\n Hartree → Rydberg factor, derived from the built-in EnergyUnitSystem so\n * there is a single source of truth for conversion factors.\n \n This resolves to exactly 2 (27.2114/13.6057 in floating point), which is\n * what keeps same-format round-trips bit-exact. The factor is resolved ONCE\n * here and hot loops multiply by it directly — never call\n * EnergyUnitSystem.convert per value: it performs alias lookups plus two\n * roundings per call, so (v27.2114)/13.6057 differs from v2 by 1 ulp for\n * some doubles (e.g. -4.8696255250391e-8) and costs a call per element.\n * See the \"pseudo units\" benchmarks for the measured gap.\n /\nexport const HARTREE_TO_RYDBERG: number = EnergyUnitSystem.convert(\n 1,\n \"Hartree\",\n \"Rydberg\",\n);\n\n/* Rydberg → Hartree factor, derived from the built-in EnergyUnitSystem (exactly 0.5). /\nexport const RYDBERG_TO_HARTREE: number = EnergyUnitSystem.convert(\n 1,\n \"Rydberg\",\n \"Hartree\",\n);\n\n/* Alias used in adapters: energies stored in Hartree files → canonical Ry. /\nexport const HA_TO_RY = HARTREE_TO_RYDBERG;\n\n/* Alias used in adapters: canonical Ry → Hartree for file output. /\nexport const RY_TO_HA = RYDBERG_TO_HARTREE;\n\n/* Scale a single energy value (Hartree → Ry). /\nexport function haToRy(value: number): number {\n return value HA_TO_RY;\n}\n\n/** Scale a single energy value (Ry → Hartree). /\nexport function ryToHa(value: number): number {\n return value RY_TO_HA;\n}\n\n/** Scale every entry of an energy array (Hartree → Ry), returning a new array. /\nexport function haArrayToRy(values: Float64Array): Float64Array {\n const out = new Float64Array(values.length);\n for (let i = 0; i < values.length; i++) out[i] = values[i] HA_TO_RY;\n return out;\n}\n\n/** Scale every entry of an energy array (Ry → Hartree), returning a new array. /\nexport function ryArrayToHa(values: Float64Array): Float64Array {\n const out = new Float64Array(values.length);\n for (let i = 0; i < values.length; i++) out[i] = values[i] RY_TO_HA;\n return out;\n}\n\n/*\n Energy-carrying fields converted when crossing the Hartree boundary.\n \n Converted (energies, in Ry canonically):\n * header.totalPsenergy / wfcCutoff / rhoCutoff, local.vloc, semilocal vnl,\n * D_ij values, wfc pseudoEnergy, paw.coreEnergy, paw.aeVloc,\n * gth.cexpPpl / hprj / kprj.\n \n NOT converted (lengths, densities, dimensionless shapes):\n * mesh r/rab/rmax/dx/xmin/zmesh, cutoff radii, rhoatom, nlcc, occupations,\n * chi/aewfc wavefunctions and beta projectors (L²-normalized shapes, plus\n * their Gaussian tails reach denormal magnitudes that no scaling round-trips\n * bit-exactly), gth rLoc/rPs/nElec.\n /\n\n/\n Scale all energy-carrying fields of a Hartree-sourced pseudopotential to\n * canonical Ry. Mutates in place and returns the same object.\n /\nexport function scaleHaToRy(pp: Pseudopotential): Pseudopotential {\n const h = pp.header;\n h.totalPsenergy = haToRy(h.totalPsenergy);\n h.wfcCutoff = haToRy(h.wfcCutoff);\n h.rhoCutoff = haToRy(h.rhoCutoff);\n pp.local.vloc = haArrayToRy(pp.local.vloc);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) sl.vnl = haArrayToRy(sl.vnl);\n }\n for (const entry of pp.nonlocal.dij) entry[2] = haToRy(entry[2]);\n for (const wfc of pp.pswfc) {\n if (wfc.pseudoEnergy != null) wfc.pseudoEnergy = haToRy(wfc.pseudoEnergy);\n }\n if (pp.paw) {\n pp.paw.coreEnergy = haToRy(pp.paw.coreEnergy);\n pp.paw.aeVloc = haArrayToRy(pp.paw.aeVloc);\n }\n if (pp.gth) {\n pp.gth.cexpPpl = pp.gth.cexpPpl.map(haToRy);\n pp.gth.hprj = pp.gth.hprj.map((m) => m.map((row) => row.map(haToRy)));\n if (pp.gth.kprj) {\n pp.gth.kprj = pp.gth.kprj.map((m) => m.map((row) => row.map(haToRy)));\n }\n }\n return pp;\n}\n\n/\n Scale all energy-carrying fields of a canonical (Ry) pseudopotential back\n * to Hartree for Hartree-based file output. Mutates in place.\n /\nexport function scaleRyToHa(pp: Pseudopotential): Pseudopotential {\n const h = pp.header;\n h.totalPsenergy = ryToHa(h.totalPsenergy);\n h.wfcCutoff = ryToHa(h.wfcCutoff);\n h.rhoCutoff = ryToHa(h.rhoCutoff);\n pp.local.vloc = ryArrayToHa(pp.local.vloc);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) sl.vnl = ryArrayToHa(sl.vnl);\n }\n for (const entry of pp.nonlocal.dij) entry[2] = ryToHa(entry[2]);\n for (const wfc of pp.pswfc) {\n if (wfc.pseudoEnergy != null) wfc.pseudoEnergy = ryToHa(wfc.pseudoEnergy);\n }\n if (pp.paw) {\n pp.paw.coreEnergy = ryToHa(pp.paw.coreEnergy);\n pp.paw.aeVloc = ryArrayToHa(pp.paw.aeVloc);\n }\n if (pp.gth) {\n pp.gth.cexpPpl = pp.gth.cexpPpl.map(ryToHa);\n pp.gth.hprj = pp.gth.hprj.map((m) => m.map((row) => row.map(ryToHa)));\n if (pp.gth.kprj) {\n pp.gth.kprj = pp.gth.kprj.map((m) => m.map((row) => row.map(ryToHa)));\n }\n }\n return pp;\n}\n","import { PeriodicTable } from \"../../data/periodictable/atomicData\";\n\n/* Reverse lookup: element symbol → atomic number. /\nconst SymbolToZ = new Map<string, number>();\nfor (const [z, info] of Object.entries(PeriodicTable)) {\n SymbolToZ.set(info.symbol, Number(z));\n}\n\n/* Return the element symbol for a given atomic number (1-based). Returns \"X\" if unknown. /\nexport function guessElement(z: number): string {\n const info = PeriodicTable[Math.round(z)];\n return info?.symbol ?? \"X\";\n}\n\n/* Return the atomic number for a given element symbol. Returns 0 if unknown. /\nexport function elementToZ(element: string): number {\n return SymbolToZ.get(element) ?? 0;\n}\n\n/\n Map an ABINIT numeric XC code (pspxc) to a functional name.\n \n Shared by the PSP8 and FHI adapters. Unknown codes fall back to `xc=<n>`.\n /\nexport function pspxcToFunctional(pspxc: number): string {\n const map: Record<number, string> = {\n 1: \"LDA (PW)\",\n 2: \"LDA (PW92)\",\n 6: \"LDA (Wigner)\",\n 7: \"PW92\",\n 11: \"PBE\",\n 14: \"PBEsol\",\n 23: \"B3LYP\",\n };\n return map[pspxc] ?? `xc=${pspxc}`;\n}\n\n/\n Reverse-map a functional name to an ABINIT numeric XC code.\n \n Used when writing PSP8 for objects from formats that store the functional\n * as a string (e.g. via a UPF hop). Returns undefined when unknown.\n /\nexport function functionalToPspxc(functional: string): number \| undefined {\n const map: Record<string, number> = {\n \"LDA (PW)\": 1,\n \"LDA (PW92)\": 2,\n \"LDA (Wigner)\": 6,\n PW92: 7,\n PBE: 11,\n PBEsol: 14,\n B3LYP: 23,\n };\n return map[functional];\n}\n","/\n FHI98PP (.cpi / .fhi) pseudopotential adapter.\n \n Converts between FHI text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n The FHI format stores norm-conserving pseudopotentials in semilocal form\n * on a logarithmic radial grid. Native units: Hartree (energy), Bohr\n * (length) — energies are converted to Ry on parse (×2) and back on\n * serialize (×0.5).\n \n Grid formula: r(i) = (exp(dx * i) - 1) / Z_eff\n * Stored data: V_l(r) = r * [V_nl(r) + Z_ion/r] (semilocal with Coulomb tail)\n \n Loss notes: raw .cpi carries no element symbol or XC name; those fields\n * stay empty. Only semilocal KB-free data is representable, so objects with\n * projectors/D_ij/US/PAW lose that data here; `canWriteFHI()` reports\n * whether conversion is safe.\n \n References:\n * - Fuchs & Scheffler, Comput. Phys. Commun. 119, 67 (1999)\n * - ABINIT format 6: .fhi = ABINIT header + .cpi content\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement, pspxcToFunctional } from \"./elements\";\n\nexport interface FHIConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as FHI.\n * FHI stores norm-conserving semilocal data only.\n /\nexport function canWriteFHI(pp: Pseudopotential): FHIConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType === \"PAW\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.betas.length > 0 \|\| pp.nonlocal.dij.length > 0) {\n reasons.push(\"KB projectors/D_ij have no FHI representation\");\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no FHI representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no FHI representation\");\n }\n if (pp.paw \|\| pp.fullWfc) {\n reasons.push(\"PAW data has no FHI representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse an FHI98PP pseudopotential file — auto-detects format.\n \n - `.fhi` format (ABINIT format 6): 7 ABINIT header lines + .cpi content\n * - `.cpi` format: starts directly with valence data\n \n Detection: if the first non-empty line starts with a digit → `.cpi`;\n * otherwise → `.fhi`.\n /\nexport function fromFHI(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\");\n const firstNonEmpty = allLines.find((l) => l.trim().length > 0);\n if (!firstNonEmpty) throw new Error(\"FHI file too short to parse\");\n\n // .fhi format (ABINIT format 6) starts with a text description.\n // .cpi format starts with a number (Z_val).\n if (/^\\s\\d/.test(firstNonEmpty)) {\n return parseCpi(text);\n }\n return parseFhiHeader(text);\n}\n\n/*\n Parse a raw .cpi body (without ABINIT header).\n \n Format:\n * Line 1: Z_val n_components\n * Lines 2+: legacy zero-header (variable length, scanned for the mesh line)\n * Then: index r(i) V_0(i) V_1(i) ... V_{lmax}(i) [f_core f_core' f_core'']\n /\nfunction parseCpi(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 4) {\n throw new Error(\"FHI file too short to parse\");\n }\n\n // Line 1: Z_val, n_components\n const line1 = allLines[0].trim().split(/\\s+/);\n const zValence = parseFortranNumber(line1[0]);\n const nComponents = parseIntSafe(line1[1]);\n const lMax = nComponents - 1;\n\n // Lines 2+: legacy header (variable number of zero lines).\n // Scan for the mesh line: first token is a positive integer (mesh_max),\n // second token is a floating-point number (dx).\n let meshLineIdx = 1;\n for (; meshLineIdx < allLines.length; meshLineIdx++) {\n const parts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 2) {\n const firstInt = parseIntSafe(parts[0]);\n if (firstInt > 0) break;\n }\n }\n const meshParts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n const meshMax = parseIntSafe(meshParts[0]);\n const dx = parseFortranNumber(meshParts[1]);\n\n // Parse data block (lines after mesh line)\n // Columns: index, r(i), V_0(i), V_1(i), ... [, f_core, f_core', f_core'']\n const rValues: number[] = [];\n const semilocal: Float64Array[] = [];\n for (let l = 0; l <= lMax; l++) {\n semilocal.push(new Float64Array(meshMax));\n }\n let hasNlcc = false;\n const nlccData: number[] = [];\n\n for (let i = meshLineIdx + 1; i < allLines.length && rValues.length < meshMax; i++) {\n const parts = allLines[i].trim().split(/\\s+/).filter(Boolean);\n if (parts.length < 3) continue;\n\n const idx = parseIntSafe(parts[0]);\n const r = parseFortranNumber(parts[1]);\n\n // Semilocal potentials\n for (let l = 0; l <= lMax && l + 2 < parts.length; l++) {\n semilocal[l][rValues.length] = parseFortranNumber(parts[l + 2]);\n }\n\n // NLCC data (columns after semilocal potentials)\n const nlccStart = nComponents + 2;\n if (parts.length > nlccStart) {\n hasNlcc = true;\n nlccData.push(parseFortranNumber(parts[nlccStart]));\n }\n\n rValues.push(r);\n }\n\n // Build mesh\n const r = new Float64Array(rValues);\n const rmax = r[r.length - 1];\n\n // Compute rab (dr/di) from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n dx,\n rmax,\n r,\n rab,\n };\n\n // Convert semilocal potentials Hartree → Ry. The l=0 channel doubles as\n // the local part (the FHI format has no separate local potential).\n const semilocalRy = semilocal.map(haArrayToRy);\n const local: PseudopotentialLocal = {\n vloc: semilocalRy.length > 0 ? semilocalRy[0] : new Float64Array(r.length),\n };\n\n // Store semilocal potentials\n const semilocalPotentials = semilocalRy.map((vnl, l) => ({\n l,\n vnl,\n }));\n\n // No KB projectors from FHI format — store as semilocal\n const nonlocal: PseudopotentialNonlocal = {\n betas: [],\n dij: [],\n };\n\n // Build rhoatom (approximate from semilocal if available)\n const rhoatom = new Float64Array(r.length);\n\n return {\n format: \"CPI\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"CPI\" },\n header: {\n element: \"\",\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: hasNlcc,\n functional: \"\",\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: 0,\n numberOfProj: 0,\n },\n mesh,\n local,\n semilocal: semilocalPotentials,\n nonlocal,\n pswfc: [],\n rhoatom,\n nlcc: hasNlcc ? new Float64Array(nlccData) : undefined,\n };\n}\n\n/\n Parse an FHI .fhi file (ABINIT format 6).\n * Skips the 7 ABINIT header lines, then parses the .cpi body.\n /\nfunction parseFhiHeader(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\");\n if (allLines.length < 8) {\n throw new Error(\"FHI file too short to parse (.fhi needs 7 header lines)\");\n }\n // Skip 7 ABINIT header lines, then parse as .cpi\n const cpiContent = allLines.slice(7).join(\"\\n\");\n const pp = parseCpi(cpiContent);\n\n pp.provenance = {\n ...pp.provenance,\n notes: \"parsed from .fhi (ABINIT format 6) envelope\",\n };\n\n // Extract metadata from ABINIT header\n const line2 = allLines[1].trim().split(/\\s+/);\n if (line2.length >= 1) {\n const zatom = parseFloat(line2[0]);\n if (zatom > 0) pp.header.element = guessElement(zatom);\n }\n if (line2.length >= 2) {\n pp.header.zValence = parseFloat(line2[1]);\n }\n\n const line3 = allLines[2].trim().split(/\\s+/);\n if (line3.length >= 3) {\n // pspcod should be 6 for FHI\n const pspxc = parseIntSafe(line3[1]);\n pp.header.xcCode = pspxc;\n pp.header.functional = pspxcToFunctional(pspxc);\n }\n if (line3.length >= 6) {\n pp.header.r2well = parseFortranNumber(line3[5]);\n }\n\n const line4 = allLines[3].trim().split(/\\s+/);\n if (line4.length >= 3) {\n pp.header.rchrg = parseFortranNumber(line4[0]);\n pp.header.fchrg = parseFortranNumber(line4[1]);\n pp.header.qchrg = parseFortranNumber(line4[2]);\n }\n\n return pp;\n}\n\n/\n Serialize a first-class Pseudopotential to FHI .cpi format.\n \n Energies are written in Hartree (native .cpi units). The .cpi body carries\n * no element or functional metadata.\n /\nexport function toFHI(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const nComponents = pp.header.lMax + 1;\n const r = pp.mesh.r;\n\n // Line 1: Z_val, n_components\n lines.push(`${formatFortranNumber(pp.header.zValence, 20)} ${nComponents}`);\n\n // Lines 2-10: legacy header (zeros)\n for (let i = 0; i < 9; i++) {\n lines.push(\" 0.0000 0.0000 0.0000 0.0000\");\n }\n\n // Line 11: mesh_max, dx\n const dx = pp.mesh.dx ?? 0.01;\n lines.push(`${r.length.toString().padStart(6)} ${formatFortranNumber(dx, 20)}`);\n\n // Data block\n for (let i = 0; i < r.length; i++) {\n const parts: string[] = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(r[i], 20),\n ];\n\n // Semilocal potentials (Ry → Ha) or local potential for all channels\n if (pp.semilocal && pp.semilocal.length > 0) {\n for (let l = 0; l <= pp.header.lMax; l++) {\n const sl = pp.semilocal.find((s) => s.l === l);\n parts.push(formatFortranNumber((sl ? sl.vnl[i] : 0) RY_TO_HA, 20));\n }\n } else {\n // Use local potential for all channels\n for (let l = 0; l <= pp.header.lMax; l++) {\n parts.push(formatFortranNumber(pp.local.vloc[i] * RY_TO_HA, 20));\n }\n }\n\n // NLCC data (densities are unit-free)\n if (pp.nlcc && i < pp.nlcc.length) {\n parts.push(formatFortranNumber(pp.nlcc[i], 20));\n }\n\n lines.push(parts.join(\" \"));\n }\n\n return lines.join(\"\\n\");\n}\n","/*\n PSP8 (ABINIT format 8) pseudopotential adapter.\n \n PSP8 is a norm-conserving pseudopotential format produced by ONCVPSP\n * and used widely in the ABINIT/PseudoDojo ecosystem. This adapter converts\n * between PSP8 text and the first-class Pseudopotential object (canonical\n * units Ry / Bohr).\n \n Native units: Hartree (energy), Bohr (length). Energies are converted to\n * Ry on parse (×2) and back to Hartree on serialize (×0.5).\n * Grid: Linear, r(i) = (i-1) * dr, starting at r=0.\n \n Loss notes: PSP8 carries only KB projectors (no semilocal, no PAW, no\n * augmentation charge, no pseudo-wavefunctions). US/PAW objects cannot be\n * faithfully written; `canWritePSP8()` reports whether conversion is safe.\n \n Reference: https://docs.abinit.org/developers/psp8_info/\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement, elementToZ, pspxcToFunctional, functionalToPspxc } from \"./elements\";\n\nexport interface PSP8ConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as PSP8.\n * PSP8 supports norm-conserving KB data only: no US/PAW, no augmentation,\n * no spin-orbit coupling, no semilocal potentials.\n /\nexport function canWritePSP8(pp: Pseudopotential): PSP8ConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType !== \"NC\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no PSP8 representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no PSP8 representation\");\n }\n if (pp.semilocal && pp.semilocal.length > 0) {\n reasons.push(\"semilocal potentials are not written to PSP8\");\n }\n if (pp.paw \|\| pp.fullWfc) {\n reasons.push(\"PAW data has no PSP8 representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse a PSP8 pseudopotential file into a first-class Pseudopotential.\n \n Structure:\n * Header (6-7 lines):\n * Line 1: title\n * Line 2: zatom, zion, pspd\n * Line 3: pspcod(=8), pspxc, lmax, lloc, mmax, r2well\n * Line 4: rchrg, fchrg, qchrg\n * Line 5: nproj(0..lmax)\n * Line 6: extension_switch\n * Line 7 (if extension_switch=2 or 3): nprojso(1..lmax)\n \n Data blocks:\n * For each l with nproj(l) > 0: projector block\n * Local potential block\n * If extension_switch=2 or 3: SO projector blocks\n * If fchrg > 0: NLCC block\n /\nexport function fromPSP8(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 6) {\n throw new Error(\"PSP8 file too short to parse\");\n }\n\n let lineIdx = 0;\n\n // Line 1: title\n const title = allLines[lineIdx++].trim();\n\n // Line 2: zatom, zion, pspd\n const line2 = allLines[lineIdx++].trim().split(/\\s+/);\n const zatom = parseFortranNumber(line2[0]);\n const zion = parseFortranNumber(line2[1]);\n const pspd = line2.length > 2 ? line2[2] : \"\";\n\n // Line 3: pspcod, pspxc, lmax, lloc, mmax, r2well\n const line3 = allLines[lineIdx++].trim().split(/\\s+/);\n const pspcod = parseIntSafe(line3[0]);\n if (pspcod !== 8) {\n throw new Error(`Expected pspcod=8 for PSP8 format, got ${pspcod}`);\n }\n const pspxc = parseIntSafe(line3[1]);\n const lmax = parseIntSafe(line3[2]);\n const lloc = parseIntSafe(line3[3]);\n const mmax = parseIntSafe(line3[4]);\n const r2well = line3.length > 5 ? parseFortranNumber(line3[5]) : undefined;\n\n // Line 4: rchrg, fchrg, qchrg\n const line4 = allLines[lineIdx++].trim().split(/\\s+/);\n const rchrg = parseFortranNumber(line4[0]);\n const fchrg = parseFortranNumber(line4[1]);\n const qchrg = line4.length > 2 ? parseFortranNumber(line4[2]) : 0;\n\n // Line 5: nproj(0..lmax)\n const line5 = allLines[lineIdx++].trim().split(/\\s+/);\n const nproj: number[] = [];\n for (let l = 0; l <= lmax; l++) {\n nproj.push(l < line5.length ? parseIntSafe(line5[l]) : 0);\n }\n\n // Line 6: extension_switch\n const extensionSwitch = parseIntSafe(allLines[lineIdx++].trim());\n\n // Line 7 (if SO): nprojso(1..lmax)\n const nprojso: number[] = [];\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n const line7 = allLines[lineIdx++].trim().split(/\\s+/);\n for (let l = 1; l <= lmax; l++) {\n nprojso.push(l - 1 < line7.length ? parseIntSafe(line7[l - 1]) : 0);\n }\n }\n\n const hasSo = extensionSwitch === 2 \|\| extensionSwitch === 3;\n const hasRhoatom = extensionSwitch === 1 \|\| extensionSwitch === 3;\n\n // Read the radial grid from the first data block (all blocks share it).\n // We collect r(i) here as blocks are consumed, then validate at the end.\n const rValues = new Float64Array(mmax);\n\n const readDataBlock = (\n cols: number,\n skipHeader = true,\n ): { headerParts: string[]; grid: Float64Array; data: Float64Array[] } => {\n const headerParts = skipHeader\n ? allLines[lineIdx++].trim().split(/\\s+/)\n : [];\n const grid = new Float64Array(mmax);\n const data: Float64Array[] = [];\n for (let p = 0; p < cols; p++) data.push(new Float64Array(mmax));\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 2) grid[i] = parseFortranNumber(parts[1]);\n for (let p = 0; p < cols && p + 2 < parts.length; p++) {\n data[p][i] = parseFortranNumber(parts[p + 2]);\n }\n }\n return { headerParts, grid, data };\n };\n\n // Parse projector blocks and local potential\n const betas: BetaProjector[] = [];\n let localVloc: Float64Array = new Float64Array(mmax);\n const ekbValues: number[][] = [];\n let gridSet = false;\n\n const adoptGrid = (grid: Float64Array): void => {\n if (!gridSet) {\n rValues.set(grid);\n gridSet = true;\n }\n };\n\n // Data blocks appear in l order. If lloc <= lmax, the local potential\n // replaces the projector block at position lloc.\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) {\n // Local potential block: header line carries just the l value.\n const { headerParts, grid, data } = readDataBlock(1);\n void headerParts;\n adoptGrid(grid);\n localVloc = data[0];\n } else if (nproj[l] > 0) {\n // Projector block: header line is \"l ekb(1) ekb(2) ...\".\n const { headerParts, grid, data } = readDataBlock(nproj[l]);\n adoptGrid(grid);\n const blockL = parseIntSafe(headerParts[0]);\n const ekb: number[] = [];\n for (let p = 1; p < headerParts.length; p++) {\n ekb.push(parseFortranNumber(headerParts[p]));\n }\n ekbValues.push(ekb);\n\n // Create one beta projector per ekb value. Beta arrays are\n // L2-normalized shapes and stay in file units; energies (ekb, vloc)\n // convert separately.\n for (let p = 0; p < nproj[l]; p++) {\n betas.push({\n angularMomentum: Number.isNaN(blockL) ? l : blockL,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}`,\n beta: data[p],\n });\n }\n }\n }\n\n // If lloc > lmax, local potential comes after all projector blocks\n if (lloc > lmax) {\n const { grid, data } = readDataBlock(1);\n adoptGrid(grid);\n localVloc = data[0];\n }\n localVloc = haArrayToRy(localVloc);\n\n // Build D_ij matrix (Ha → Ry) from ekb values.\n // For single projectors per l: dij[i][i] = ekb[i]; block-diagonal otherwise.\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n let ekbIdx = 0;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) continue;\n if (nproj[l] > 0) {\n const nProjL = nproj[l];\n const ekbL = ekbValues[ekbIdx++] ?? [];\n for (let i = 0; i < nProjL; i++) {\n for (let j = 0; j < nProjL; j++) {\n const val = i === j ? haToRy(ekbL[i] ?? 1.0) : 0;\n dij.push([projIdx + i, projIdx + j, val]);\n }\n }\n projIdx += nProjL;\n }\n }\n\n // Parse SO projector blocks (extension_switch == 2 or 3).\n // ekbso values are stored as diagonal D_ij entries for the \"-so\" projectors.\n if (hasSo) {\n for (let l = 1; l <= lmax; l++) {\n const nProjSo = nprojso[l - 1] ?? 0;\n if (nProjSo > 0) {\n const { headerParts, data } = readDataBlock(nProjSo);\n const soEkb: number[] = [];\n for (let p = 1; p < headerParts.length; p++) {\n soEkb.push(parseFortranNumber(headerParts[p]));\n }\n for (let p = 0; p < nProjSo; p++) {\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}-so`,\n beta: data[p],\n });\n dij.push([projIdx + p, projIdx + p, haToRy(soEkb[p] ?? 1.0)]);\n }\n projIdx += nProjSo;\n }\n }\n }\n\n // Parse NLCC block if present (no header line — mmax bare data lines)\n let nlcc: Float64Array \| undefined;\n if (fchrg > 0) {\n const { data } = readDataBlock(1, false);\n nlcc = data[0];\n }\n\n // Parse pseudo valence charge block if extension_switch == 1 or 3\n // (no header line — mmax bare data lines)\n const rhoatom = new Float64Array(mmax);\n if (hasRhoatom) {\n const { data } = readDataBlock(1, false);\n rhoatom.set(data[0]);\n }\n\n // Build mesh (linear grid, Bohr)\n const rmax = rValues[mmax - 1] \|\| 0;\n const dr = mmax > 1 && rmax > 0 ? rValues[1] - rValues[0] : 0;\n const rab = new Float64Array(mmax).fill(dr);\n\n const mesh: PseudopotentialMesh = {\n gridType: \"linear\",\n rmax,\n r: rValues,\n rab,\n };\n\n // Guess element from zatom\n const element = guessElement(zatom);\n\n // Map pspxc to functional string\n const functional = pspxcToFunctional(pspxc);\n\n return {\n format: \"PSP8\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"PSP8\", creator: title, date: pspd },\n header: {\n element,\n generated: title,\n date: pspd,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: fchrg > 0,\n functional,\n zValence: zion,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: lmax,\n lMaxRho: lmax,\n lLocal: lloc,\n meshSize: mmax,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n xcCode: pspxc,\n extensionSwitch,\n r2well,\n rchrg,\n fchrg,\n qchrg,\n },\n mesh,\n local: { vloc: localVloc } satisfies PseudopotentialLocal,\n nonlocal: { betas, dij } satisfies PseudopotentialNonlocal,\n pswfc: [],\n rhoatom,\n nlcc,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to PSP8 format.\n \n Energies (vloc, projectors, ekb) are written back in Hartree. Only\n * norm-conserving data is supported; use `canWritePSP8()` to check first.\n /\nexport function toPSP8(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const lmax = pp.header.lMax;\n const mmax = pp.mesh.r.length;\n // QE uses lLocal < 0 for \"no explicit local channel\"; PSP8 has no such\n // notion, so map it to \"separate local block\" (lloc > lmax), which carries\n // the same semantics (local potential tabulated on its own).\n const rawLloc = pp.header.lLocal ?? 0;\n const lloc = rawLloc < 0 ? lmax + 1 : rawLloc;\n\n // Split betas into regular and spin-orbit groups (label suffix \"-so\").\n const isSoBeta = (b: BetaProjector): boolean => b.label.endsWith(\"-so\");\n const regularBetas = pp.nonlocal.betas.filter((b) => !isSoBeta(b));\n const soBetas = pp.nonlocal.betas.filter(isSoBeta);\n\n const nproj: number[] = new Array(lmax + 1).fill(0);\n for (const beta of regularBetas) {\n if (beta.angularMomentum <= lmax && beta.angularMomentum >= 0) {\n nproj[beta.angularMomentum]++;\n }\n }\n const nprojso: number[] = new Array(Math.max(lmax, 0)).fill(0);\n for (const beta of soBetas) {\n if (beta.angularMomentum >= 1 && beta.angularMomentum <= lmax) {\n nprojso[beta.angularMomentum - 1]++;\n }\n }\n\n // extension_switch: prefer the stored value; derive it for objects from\n // formats without the concept (e.g. UPF) from the data actually present.\n const hasRhoatomData = pp.rhoatom.some((v) => v !== 0);\n const extensionSwitch =\n pp.header.extensionSwitch ??\n (hasRhoatomData ? 1 : 0) + (soBetas.length > 0 ? 2 : 0);\n\n // Header\n const zatom = elementToZ(pp.header.element);\n lines.push(pp.header.generated ?? `${pp.header.element} ${pp.header.functional}`);\n const pspd = pp.header.date ?? \"000000\";\n lines.push(\n `${zatom.toFixed(4).padStart(12)} ${pp.header.zValence.toFixed(4).padStart(12)} ${pspd.padStart(8)}`,\n );\n // XC code: prefer the stored value; reverse-map the functional string for\n // objects arriving via formats that only carry the name (e.g. UPF).\n const pspxc =\n pp.header.xcCode ?? functionalToPspxc(pp.header.functional) ?? 0;\n lines.push(\n ` 8 ${pspxc} ${lmax} ${lloc} ${mmax} ${pp.header.r2well ?? 0}`,\n );\n const rchrg = pp.header.rchrg ?? 0;\n const fchrg =\n pp.header.fchrg ?? (pp.nlcc ? 1.0 : pp.header.coreCorrection ? 1.0 : 0.0);\n const qchrg = pp.header.qchrg ?? 0;\n lines.push(`${rchrg.toFixed(4).padStart(12)} ${fchrg.toFixed(4).padStart(12)} ${qchrg.toFixed(4).padStart(12)}`);\n lines.push(` ${nproj.join(\" \")}`);\n lines.push(` ${extensionSwitch}`);\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n lines.push(` ${nprojso.join(\" \")}`);\n }\n\n // Projector blocks (regular). ekb recovered from diagonal D_ij entries.\n const ekb = pp.nonlocal.dij;\n const ekbOf = (globalIdx: number): number => {\n const entry = ekb.find(([nb, mb]) => nb === globalIdx && mb === globalIdx);\n return entry ? entry[2] RY_TO_HA : 1.0;\n };\n\n let projOffset = 1;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) {\n // Local potential replaces the block at the lloc position.\n lines.push(` ${l}`);\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.local.vloc[i] * RY_TO_HA)}`,\n );\n }\n continue;\n }\n const lBetas = regularBetas.filter((b) => b.angularMomentum === l);\n if (lBetas.length === 0) continue;\n\n const ekbValues = lBetas.map((_, i) => ekbOf(projOffset + i));\n lines.push(` ${l} ${ekbValues.map((e) => formatFortranNumber(e)).join(\" \")}`);\n\n for (let i = 0; i < mmax; i++) {\n const parts = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(pp.mesh.r[i]),\n ];\n for (const beta of lBetas) {\n parts.push(formatFortranNumber(beta.beta[i] ?? 0));\n }\n lines.push(parts.join(\" \"));\n }\n\n projOffset += lBetas.length;\n }\n\n // Local potential block (Hartree) — only when it does not replace a\n // channel block above (lloc > lmax means a separate trailing block).\n if (lloc > lmax) {\n lines.push(` ${lloc}`);\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.local.vloc[i] * RY_TO_HA)}`,\n );\n }\n }\n\n // SO projector blocks\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n for (let l = 1; l <= lmax; l++) {\n const lBetas = soBetas.filter((b) => b.angularMomentum === l);\n if (lBetas.length === 0) continue;\n const ekbValues = lBetas.map((_, i) => ekbOf(projOffset + i));\n lines.push(` ${l} ${ekbValues.map((e) => formatFortranNumber(e)).join(\" \")}`);\n for (let i = 0; i < mmax; i++) {\n const parts = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(pp.mesh.r[i]),\n ];\n for (const beta of lBetas) {\n parts.push(formatFortranNumber(beta.beta[i] ?? 0));\n }\n lines.push(parts.join(\" \"));\n }\n projOffset += lBetas.length;\n }\n }\n\n // NLCC block\n if (pp.nlcc) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.nlcc[i])}`,\n );\n }\n }\n\n // Pseudo valence charge block (if extension_switch == 1 or 3)\n if (extensionSwitch === 1 \|\| extensionSwitch === 3) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.rhoatom[i])}`,\n );\n }\n }\n\n return lines.join(\"\\n\");\n}\n","/*\n PSML (PSeudopotential Markup Language) pseudopotential adapter.\n \n Converts between PSML text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n PSML is an XML-based format for norm-conserving pseudopotentials,\n * created by the ESL (Electronic Structure Library) initiative.\n * Native units: Hartree (energy), Bohr (length) — mandatory per schema.\n * Energies are converted to Ry on parse (×2) and back on serialize (×0.5).\n \n Loss notes: PSML stores only the diagonal KB energies (ekb); off-diagonal\n * D_ij couplings have no representation. PAW/US/augmentation/spin-orbit\n * data cannot round-trip; use `canWritePSML()` to check first.\n \n Reference: https://siesta-project.github.io/psml-docs/\n * Schema: http://esl.cecam.org/PSML/ns/1.2\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n Provenance,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n textOf,\n toArray,\n parseXml,\n} from \"./xml-helpers\";\n\nimport { guessElement, elementToZ } from \"./elements\";\n\nexport interface PSMLConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as PSML.\n * PSML supports norm-conserving data only.\n /\nexport function canWritePSML(pp: Pseudopotential): PSMLConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType !== \"NC\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no PSML representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no PSML representation\");\n }\n if (pp.paw \|\| pp.fullWfc \|\| pp.gipaw) {\n reasons.push(\"PAW/GIPAW data has no PSML representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse a PSML pseudopotential file into a first-class Pseudopotential.\n /\nexport function fromPSML(text: string): Pseudopotential {\n const parsed = parseXml(text);\n\n // Find root element (may have namespace prefix)\n const root = parsed[\"psml\"] ?? parsed[`${\"http://esl.cecam.org/PSML/ns/1.2\"}:psml`] ?? parsed;\n\n // Provenance\n const provenanceData = root[\"provenance\"];\n let creator: string \| undefined;\n let date: string \| undefined;\n if (provenanceData) {\n const provArr = toArray(provenanceData);\n if (provArr.length > 0) {\n const first = provArr[0];\n creator = attr(first, \"creator\") \|\| undefined;\n date = attr(first, \"date\") \|\| undefined;\n }\n }\n const provenance: Provenance = { sourceFormat: \"PSML\", creator, date };\n\n // Pseudo-atom spec\n const spec = root[\"pseudo-atom-spec\"] ?? {};\n const element = attr(spec, \"atomic-label\") \|\| guessElement(attrInt(spec, \"atomic-number\"));\n const zValence = attrNum(spec, \"z-pseudo\");\n const relativity = attr(spec, \"relativity\") \|\| \"scalar\";\n const coreCorrections = attr(spec, \"core-corrections\") === \"yes\";\n\n // XC functional from libxc-info\n const xcInfo = spec[\"exchange-correlation\"]?.[\"libxc-info\"];\n let functional = \"\";\n if (xcInfo) {\n const funchs = toArray(xcInfo[\"functional\"]);\n functional = funchs.map((f: XmlNode) => attr(f, \"name\")).join(\"+\");\n }\n\n // Grid\n const gridNode = root[\"grid\"];\n let r: Float64Array = new Float64Array(0);\n if (gridNode) {\n const gridData = gridNode[\"grid-data\"];\n if (gridData) r = parseFloat64Array(textOf(gridData));\n }\n if (r.length === 0) throw new Error(\"Missing or empty grid in PSML file\");\n\n // Compute rab from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"custom\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Local potential (Hartree → Ry)\n const localNode = root[\"local-potential\"];\n let localVloc: Float64Array = new Float64Array(r.length);\n if (localNode) {\n const dataNode = localNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) localVloc = haArrayToRy(parseFloat64Array(textOf(dataNode)));\n }\n\n // Semilocal potentials (Hartree → Ry)\n const slNode = root[\"semilocal-potentials\"];\n const semilocalPotentials: Pseudopotential[\"semilocal\"] = [];\n const slSet = toArray(slNode);\n if (slSet.length > 0) {\n const slpsNodes = toArray(slSet[0][\"slps\"]);\n for (const slps of slpsNodes) {\n const l = lFromLetter(attr(slps, \"l\"));\n const dataNode = slps[\"radfunc\"]?.[\"data\"];\n const vnl = dataNode\n ? haArrayToRy(parseFloat64Array(textOf(dataNode)))\n : new Float64Array(r.length);\n semilocalPotentials.push({ l, vnl });\n }\n }\n\n // Nonlocal projectors (dimensionless shapes — no conversion)\n const nlNode = root[\"nonlocal-projectors\"];\n const betas: BetaProjector[] = [];\n const nlSet = toArray(nlNode);\n const ekbByIdx = new Map<number, number>();\n if (nlSet.length > 0) {\n const projNodes = toArray(nlSet[0][\"proj\"]);\n let idx = 1;\n for (const proj of projNodes) {\n const l = lFromLetter(attr(proj, \"l\"));\n const ekb = attrNum(proj, \"ekb\");\n ekbByIdx.set(idx, ekb);\n const dataNode = proj[\"radfunc\"]?.[\"data\"];\n const betaData = dataNode\n ? parseFloat64Array(textOf(dataNode))\n : new Float64Array(r.length);\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${lToLetter(l)}`,\n beta: betaData,\n });\n idx++;\n }\n }\n\n // Build D_ij from ekb values (diagonal; PSML stores no off-diagonal data)\n const dij: Array<[number, number, number]> = [];\n for (const [idx, ekb] of ekbByIdx) {\n dij.push([idx, idx, haToRy(ekb)]);\n }\n\n // Pseudo wavefunctions (dimensionless radial functions — no conversion)\n const pswfcNodes = toArray(root[\"pseudo-wave-functions\"]);\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcNodes.length > 0) {\n const pswfNodes = toArray(pswfcNodes[0][\"pswf\"]);\n for (const pswf of pswfNodes) {\n const l = lFromLetter(attr(pswf, \"l\"));\n const n = attrInt(pswf, \"n\");\n const dataNode = pswf[\"radfunc\"]?.[\"data\"];\n const chi = dataNode ? parseFloat64Array(textOf(dataNode)) : new Float64Array(r.length);\n pswfc.push({\n l,\n occupation: 0,\n label: `${n}${lToLetter(l)}`,\n n,\n chi,\n });\n }\n }\n\n // Valence charge (density — no conversion; store as rhoatom)\n const vcNode = root[\"valence-charge\"];\n let rhoatom: Float64Array = new Float64Array(r.length);\n if (vcNode) {\n const dataNode = vcNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) rhoatom = parseFloat64Array(textOf(dataNode));\n }\n\n // Core charge (NLCC, density — no conversion)\n const ccNode = root[\"pseudocore-charge\"];\n let nlcc: Float64Array \| undefined;\n if (ccNode) {\n const dataNode = ccNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) nlcc = parseFloat64Array(textOf(dataNode));\n }\n\n return {\n format: \"PSML\",\n units: { ...CANONICAL_UNITS },\n provenance,\n header: {\n element,\n pseudoType: \"NC\",\n relativistic: relativity as PseudopotentialHeader[\"relativistic\"],\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: coreCorrections,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: semilocalPotentials.length > 0\n ? Math.max(...semilocalPotentials.map((s) => s.l))\n : betas.length > 0\n ? Math.max(...betas.map((b) => b.angularMomentum))\n : 0,\n lMaxRho: 0,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: pswfc.length,\n numberOfProj: betas.length,\n },\n mesh,\n local: { vloc: localVloc },\n semilocal: semilocalPotentials.length > 0 ? semilocalPotentials : undefined,\n nonlocal: { betas, dij },\n pswfc,\n rhoatom,\n nlcc,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to PSML format.\n * Energies are written in Hartree (mandatory per the PSML schema).\n /\nexport function toPSML(pp: Pseudopotential): string {\n const r = pp.mesh.r;\n const npts = r.length;\n\n let xml = `<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\\n`;\n xml += `<psml version=\"1.2\" energy_unit=\"hartree\" length_unit=\"bohr\" uuid=\"matsci-parse\">\\n`;\n\n // Provenance: provenance fields take precedence; fall back to the UPF\n // header equivalents so generator stamps survive a hub conversion.\n {\n const provCreator =\n pp.provenance.creator ?? pp.header.generated ?? pp.header.author ?? \"matsci-parse\";\n const provDate =\n pp.provenance.date ?? pp.header.date ?? new Date().toISOString().split(\"T\")[0];\n xml += ` <provenance creator=\"${provCreator}\" date=\"${provDate}\">\\n`;\n xml += ` <annotation type=\"generated-by\" value=\"matsci-parse pseudopotential library\" />\\n`;\n xml += ` </provenance>\\n`;\n }\n\n // Pseudo-atom spec\n xml += ` <pseudo-atom-spec atomic-label=\"${pp.header.element}\" atomic-number=\"${elementToZ(pp.header.element)}\" z-pseudo=\"${pp.header.zValence}\" relativity=\"${pp.header.relativistic}\" core-corrections=\"${pp.header.coreCorrection ? \"yes\" : \"no\"}\">\\n`;\n if (pp.header.functional) {\n xml += ` <exchange-correlation>\\n`;\n xml += ` <libxc-info number-of-functionals=\"0\">\\n`;\n xml += ` <functional name=\"${pp.header.functional}\" />\\n`;\n xml += ` </libxc-info>\\n`;\n xml += ` </exchange-correlation>\\n`;\n }\n xml += ` </pseudo-atom-spec>\\n`;\n\n // Grid\n xml += ` <grid npts=\"${npts}\">\\n`;\n xml += ` <grid-data>\\n`;\n xml += ` ${Array.from(r).map((v) => formatFortranNumber(v).trim()).join(\" \")}\\n`;\n xml += ` </grid-data>\\n`;\n xml += ` </grid>\\n`;\n\n const ha = (v: number): string => formatFortranNumber(v RY_TO_HA).trim();\n const raw = (v: number): string => formatFortranNumber(v).trim();\n\n // Local potential (Ry → Ha)\n xml += ` <local-potential>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">\\n`;\n xml += ` ${Array.from(pp.local.vloc).map(ha).join(\" \")}\\n`;\n xml += ` </data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </local-potential>\\n`;\n\n // Semilocal potentials (Ry → Ha)\n if (pp.semilocal && pp.semilocal.length > 0) {\n xml += ` <semilocal-potentials set=\"scalar_relativistic\">\\n`;\n for (const sl of pp.semilocal) {\n xml += ` <slps l=\"${lToLetter(sl.l)}\" n=\"${sl.l + 1}\" rc=\"0\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${Array.from(sl.vnl).map(ha).join(\" \")}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </slps>\\n`;\n }\n xml += ` </semilocal-potentials>\\n`;\n }\n\n // Nonlocal projectors (shapes unconverted; ekb from diagonal D_ij).\n const nonlocal: PseudopotentialNonlocal = pp.nonlocal;\n if (nonlocal.betas.length > 0) {\n xml += ` <nonlocal-projectors set=\"scalar_relativistic\">\\n`;\n let idx = 1;\n for (const beta of nonlocal.betas) {\n const ekbEntry = nonlocal.dij.find(([nb, mb]) => nb === idx && mb === idx);\n const ekb = ekbEntry ? ekbEntry[2] * RY_TO_HA : 1.0;\n xml += ` <proj l=\"${lToLetter(beta.angularMomentum)}\" seq=\"${idx}\" ekb=\"${formatFortranNumber(ekb).trim()}\" type=\"kb\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${Array.from(beta.beta).map(raw).join(\" \")}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </proj>\\n`;\n idx++;\n }\n xml += ` </nonlocal-projectors>\\n`;\n }\n\n // Pseudo wavefunctions (dimensionless — no conversion)\n if (pp.pswfc.length > 0) {\n xml += ` <pseudo-wave-functions set=\"pseudo\">\\n`;\n for (const wfc of pp.pswfc) {\n xml += ` <pswf l=\"${lToLetter(wfc.l)}\" n=\"${wfc.n ?? wfc.l + 1}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(wfc.chi)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pswf>\\n`;\n }\n xml += ` </pseudo-wave-functions>\\n`;\n }\n\n // Valence charge\n if (pp.rhoatom.length > 0) {\n xml += ` <valence-charge total-charge=\"${pp.header.zValence}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(pp.rhoatom)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </valence-charge>\\n`;\n }\n\n // Core charge (NLCC)\n if (pp.nlcc && pp.nlcc.length > 0) {\n xml += ` <pseudocore-charge>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${pp.nlcc.length}\">${formatDataArray(pp.nlcc)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pseudocore-charge>\\n`;\n }\n\n xml += `</psml>\\n`;\n return xml;\n}\n\nfunction lFromLetter(letter: string): number {\n const map: Record<string, number> = { s: 0, p: 1, d: 2, f: 3, g: 4 };\n return map[letter.toLowerCase()] ?? 0;\n}\n\nfunction lToLetter(l: number): string {\n return \"spdfg\"[l] ?? String(l);\n}\n","import type {\n BetaProjector,\n Pseudopotential,\n PseudopotentialWfc,\n} from \"../pseudopotential\";\n\n/** One angular-momentum channel of a pseudopotential. /\nexport interface LChannel {\n /* Angular momentum. /\n l: number;\n /* KB projectors in this channel. /\n betas: BetaProjector[];\n /* Semilocal potential value for this channel, if present. /\n semilocalVnl?: Float64Array;\n /* Pseudo-wavefunctions in this channel. /\n wfcs: PseudopotentialWfc[];\n /* True when this channel is the local channel. /\n isLocal: boolean;\n}\n\n/\n Group projectors, semilocal potentials and wavefunctions by l.\n \n @param pp - The pseudopotential to inspect.\n * @returns Channels sorted by angular momentum.\n /\nexport function listChannels(pp: Pseudopotential): LChannel[] {\n const byL = new Map<number, LChannel>();\n const get = (l: number): LChannel => {\n let ch = byL.get(l);\n if (!ch) {\n ch = {\n l,\n betas: [],\n wfcs: [],\n isLocal: l === pp.header.lLocal,\n };\n byL.set(l, ch);\n }\n return ch;\n };\n for (const beta of pp.nonlocal.betas) get(beta.angularMomentum).betas.push(beta);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) get(sl.l).semilocalVnl = sl.vnl;\n }\n for (const wfc of pp.pswfc) get(wfc.l).wfcs.push(wfc);\n // Surface the local channel when it carries an l label (lLocal < 0 means\n // \"no explicit local channel\", as in some NC files).\n if (pp.header.lLocal >= 0) get(pp.header.lLocal);\n return [...byL.values()].sort((a, b) => a.l - b.l);\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/* Cutoff radii per projector (Bohr), plus header-suggested plane-wave cutoffs (Ry). /\nexport interface CutoffInfo {\n /* Per-projector cutoff radius (cutoffRadius ?? ultrasoftCutoffRadius). /\n projectorCutoffs: Array<{ l: number; label: string; cutoff: number }>;\n /* Suggested wavefunction cutoff from the header (Ry). /\n wfcCutoff: number;\n /* Suggested charge-density cutoff from the header (Ry). /\n rhoCutoff: number;\n}\n\n/\n Collect cutoff radii and suggested plane-wave cutoffs.\n \n @param pp - The pseudopotential to inspect.\n /\nexport function getCutoffs(pp: Pseudopotential): CutoffInfo {\n return {\n projectorCutoffs: pp.nonlocal.betas.map((beta) => ({\n l: beta.angularMomentum,\n label: beta.label,\n cutoff: beta.cutoffRadius ?? beta.ultrasoftCutoffRadius,\n })),\n wfcCutoff: pp.header.wfcCutoff,\n rhoCutoff: pp.header.rhoCutoff,\n };\n}\n","/* Options for radial grid generation. /\nexport interface RadialGridOptions {\n /* Number of grid points. /\n npts: number;\n /* Maximum radius in Bohr. /\n rmax: number;\n /* \"log\" mimics the GTH/log grids; \"linear\" mimics PSP8. /\n type?: \"log\" \| \"linear\";\n}\n\n/\n Generate a radial grid with trapezoidal-style integration weights.\n \n @param options - Grid size, extent and type.\n /\nexport function makeRadialGrid(options: RadialGridOptions): {\n r: Float64Array;\n rab: Float64Array;\n} {\n const { npts, rmax, type = \"log\" } = options;\n if (!Number.isInteger(npts) \|\| npts < 1) {\n throw new Error(`makeRadialGrid requires npts >= 1, got ${npts}`);\n }\n // A single-point grid is just the endpoint with zero weight.\n if (npts === 1) {\n return { r: new Float64Array([rmax]), rab: new Float64Array([0]) };\n }\n const r = new Float64Array(npts);\n const rab = new Float64Array(npts);\n if (type === \"linear\") {\n const dr = npts > 1 ? rmax / (npts - 1) : 0;\n for (let i = 0; i < npts; i++) {\n r[i] = i dr;\n rab[i] = dr;\n }\n } else {\n const dx = Math.log(rmax) / (npts - 1);\n for (let i = 0; i < npts; i++) {\n r[i] = Math.exp(dx * i);\n rab[i] = r[i] * dx;\n }\n if (npts > 1) {\n r[0] = r[1] * 0.01;\n rab[0] = r[0] * dx;\n }\n }\n return { r, rab };\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/** Piecewise-linear interpolation of y(x) at a single point. /\nfunction interp1(x: Float64Array, y: Float64Array, xi: number): number {\n if (xi <= x[0]) return y[0];\n if (xi >= x[x.length - 1]) return y[y.length - 1];\n let lo = 0;\n let hi = x.length - 1;\n while (hi - lo > 1) {\n const mid = (lo + hi) >> 1;\n if (x[mid] <= xi) lo = mid;\n else hi = mid;\n }\n const t = (xi - x[lo]) / (x[hi] - x[lo]);\n return y[lo] + t (y[hi] - y[lo]);\n}\n\n/** Resample every radial array of a pseudopotential onto a new grid. /\nfunction resampleArray(\n x: Float64Array,\n y: Float64Array,\n newX: Float64Array,\n): Float64Array {\n const out = new Float64Array(newX.length);\n for (let i = 0; i < newX.length; i++) out[i] = interp1(x, y, newX[i]);\n return out;\n}\n\n/\n Resample a pseudopotential onto a new radial grid (the grid converter).\n * Returns a new object; the header mesh counters and provenance notes are\n * updated accordingly.\n \n @param pp - The pseudopotential to resample.\n * @param newR - The new radial grid in Bohr.\n /\nexport function resampleLinear(\n pp: Pseudopotential,\n newR: Float64Array,\n): Pseudopotential {\n const oldR = pp.mesh.r;\n const rab = new Float64Array(newR.length);\n for (let i = 1; i < newR.length; i++) rab[i] = newR[i] - newR[i - 1];\n if (newR.length > 1) rab[0] = rab[1];\n\n const betas = pp.nonlocal.betas.map((beta) => ({\n ...beta,\n beta: resampleArray(oldR, beta.beta, newR),\n }));\n const semilocal = pp.semilocal?.map((sl) => ({\n ...sl,\n vnl: resampleArray(oldR, sl.vnl, newR),\n }));\n const pswfc = pp.pswfc.map((wfc) => ({\n ...wfc,\n chi: resampleArray(oldR, wfc.chi, newR),\n }));\n const fullWfc = pp.fullWfc?.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n }));\n const augmentation = pp.nonlocal.augmentation\n ? {\n ...pp.nonlocal.augmentation,\n q: pp.nonlocal.augmentation.q\n ? resampleArray(oldR, pp.nonlocal.augmentation.q, newR)\n : undefined,\n multipoles: pp.nonlocal.augmentation.multipoles\n ? resampleArray(oldR, pp.nonlocal.augmentation.multipoles, newR)\n : undefined,\n qfcoeff: pp.nonlocal.augmentation.qfcoeff\n ? resampleArray(oldR, pp.nonlocal.augmentation.qfcoeff, newR)\n : undefined,\n rinner: pp.nonlocal.augmentation.rinner\n ? resampleArray(oldR, pp.nonlocal.augmentation.rinner, newR)\n : undefined,\n qijl: pp.nonlocal.augmentation.qijl?.map((q) => ({\n ...q,\n qijl: resampleArray(oldR, q.qijl, newR),\n })),\n }\n : undefined;\n\n const resampleIfPresent = (\n arr: Float64Array \| undefined,\n ): Float64Array \| undefined =>\n arr && arr.length > 0 ? resampleArray(oldR, arr, newR) : arr;\n\n const paw = pp.paw\n ? {\n ...pp.paw,\n aeNlcc: resampleIfPresent(pp.paw.aeNlcc) ?? pp.paw.aeNlcc,\n aeVloc: resampleIfPresent(pp.paw.aeVloc) ?? pp.paw.aeVloc,\n aeWfcs: pp.paw.aeWfcs.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n })),\n psWfcs: pp.paw.psWfcs.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n })),\n }\n : undefined;\n\n const gipaw = pp.gipaw\n ? {\n ...pp.gipaw,\n coreOrbitals: pp.gipaw.coreOrbitals.map((co) => ({\n ...co,\n orbital: resampleArray(oldR, co.orbital, newR),\n })),\n orbitals: pp.gipaw.orbitals.map((orb) => ({\n ...orb,\n aeOrbital: resampleArray(oldR, orb.aeOrbital, newR),\n psOrbital: resampleArray(oldR, orb.psOrbital, newR),\n })),\n vlocAe: resampleIfPresent(pp.gipaw.vlocAe) ?? pp.gipaw.vlocAe,\n vlocPs: resampleIfPresent(pp.gipaw.vlocPs) ?? pp.gipaw.vlocPs,\n }\n : undefined;\n\n const spinOrbit = pp.spinOrbit\n ? {\n relWfcs: pp.spinOrbit.relWfcs.map((wfc) => ({\n ...wfc,\n chi: wfc.chi ? resampleArray(oldR, wfc.chi, newR) : undefined,\n })),\n relBetas: pp.spinOrbit.relBetas.map((beta) => ({\n ...beta,\n beta: beta.beta ? resampleArray(oldR, beta.beta, newR) : undefined,\n })),\n }\n : undefined;\n\n return {\n ...pp,\n header: {\n ...pp.header,\n meshSize: newR.length,\n },\n mesh: {\n ...pp.mesh,\n gridType: \"custom\",\n rmax: newR[newR.length - 1],\n r: newR,\n rab,\n },\n nlcc: pp.nlcc ? resampleArray(oldR, pp.nlcc, newR) : undefined,\n local: { vloc: resampleArray(oldR, pp.local.vloc, newR) },\n semilocal,\n nonlocal: { ...pp.nonlocal, betas, augmentation },\n pswfc,\n fullWfc,\n rhoatom: resampleArray(oldR, pp.rhoatom, newR),\n paw,\n gipaw,\n spinOrbit,\n provenance: {\n ...pp.provenance,\n notes: [\n pp.provenance.notes,\n `resampled from ${oldR.length} to ${newR.length} points`,\n ]\n .filter(Boolean)\n .join(\"; \"),\n },\n };\n}\n","import type {\n BetaProjector,\n Pseudopotential,\n} from \"../pseudopotential\";\n\nimport { listChannels } from \"./listChannels\";\n\n/\n Approximate semilocal potentials from Kleinman-Bylander projectors:\n * V_l(r) = V_loc(r) + Σ_ij β_i(r) D_ij β_j(r) / r².\n \n Note: this assumes the UPF convention of storing β(r)·r. Intended for\n * diagnostics and format bridging, not for production KB generation.\n \n @param pp - The pseudopotential with KB projectors.\n * @returns A new object with derived semilocal potentials attached.\n /\nexport function kbToSemilocal(pp: Pseudopotential): Pseudopotential {\n const r = pp.mesh.r;\n const semilocal = listChannels(pp)\n .filter((ch) => ch.betas.length > 0)\n .map((ch) => {\n const vnl = new Float64Array(r.length);\n const globalIdx = new Map<BetaProjector, number>();\n pp.nonlocal.betas.forEach((b, i) => globalIdx.set(b, i + 1));\n const dOf = (i: number, j: number): number => {\n const entry = pp.nonlocal.dij.find(\n ([nb, mb]) => nb === i && mb === j,\n );\n return entry ? entry[2] : 0;\n };\n for (let k = 0; k < r.length; k++) {\n let v = pp.local.vloc[k];\n const rk = r[k] < 1e-15 ? 1e-15 : r[k];\n for (const bi of ch.betas) {\n for (const bj of ch.betas) {\n const i = globalIdx.get(bi) ?? 0;\n const j = globalIdx.get(bj) ?? 0;\n v += (bi.beta[k] dOf(i, j) * bj.beta[k]) / (rk * rk);\n }\n }\n vnl[k] = v;\n }\n return { l: ch.l, vnl };\n });\n\n return { ...pp, semilocal };\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/*\n Approximate single-projector KB form from semilocal potentials:\n * β_l(r) = (V_l(r) − V_loc(r))·r / √\|D_l\|, D_l = ∫(V_l − V_loc) r² dr.\n \n Channels with more than one semilocal entry or a vanishing norm are\n * skipped. Intended for diagnostics and format bridging.\n \n @param pp - The pseudopotential with semilocal potentials.\n * @returns A new object with derived KB projectors appended.\n /\nexport function semilocalToKb(pp: Pseudopotential): Pseudopotential {\n const r = pp.mesh.r;\n const rab = pp.mesh.rab;\n const betas = [...pp.nonlocal.betas];\n const dij: Array<[number, number, number]> = [...pp.nonlocal.dij];\n let idx = betas.length + 1;\n\n if (pp.semilocal) {\n for (const sl of pp.semilocal) {\n const dv = new Float64Array(r.length);\n for (let k = 0; k < r.length; k++) dv[k] = sl.vnl[k] - pp.local.vloc[k];\n let d = 0;\n for (let k = 0; k < r.length; k++) d += dv[k] r[k] * r[k] * rab[k];\n if (!Number.isFinite(d) \|\| Math.abs(d) < 1e-12) continue;\n const norm = Math.sqrt(Math.abs(d));\n const sign = d >= 0 ? 1 : -1;\n const beta = new Float64Array(r.length);\n for (let k = 0; k < r.length; k++) beta[k] = (dv[k] * r[k]) / norm;\n betas.push({\n index: idx,\n angularMomentum: sl.l,\n ultrasoftCutoffRadius: r[r.length - 1],\n label: `${sl.l}${\"spdf\"[sl.l] ?? sl.l}`,\n beta,\n });\n dij.push([idx, idx, sign * Math.abs(d)]);\n idx++;\n }\n }\n\n return {\n ...pp,\n header: { ...pp.header, numberOfProj: betas.length },\n nonlocal: { ...pp.nonlocal, betas, dij },\n };\n}\n","/*\n GTH/HGH (Goedecker-Teter-Hutter / Hartwigsen-Goedecker-Hutter) adapter.\n \n Converts between GTH text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n GTH/HGH pseudopotentials are analytical, defined by Gaussian functions\n * rather than tabulated on a radial grid. The IR keeps BOTH: the analytical\n * parameters in `gth` (with `provenance.analytical = true`) and an evaluated\n * tabulation on a logarithmic grid for grid-based consumers.\n \n Native units: Hartree (energy), Bohr (length) — analytical parameters are\n * converted to Ry on parse (×2) and back on serialize (×0.5). Length-like\n * parameters (rLoc, rPs) are unit-free here (Bohr in both systems).\n \n Loss notes: k-matrix (SOC) is parsed when present (inline channel-line\n * remainder, or trailing block after the last channel) and round-trips;\n * entries without analytical GTH parameters cannot be written (`toGTH`\n * throws — use `canWriteGTH()` to check first).\n \n Reference:\n * - GTH: Goedecker, Teter, Hutter, PRB 54, 1703 (1996)\n * - HGH: Hartwigsen, Goedecker, Teter, Hutter, PRB 58, 3641 (1998)\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n GthData,\n PseudopotentialFormat,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n} from \"../../pseudopotential/units\";\n\nimport { makeRadialGrid } from \"../../pseudopotential/operations\";\n\nimport {\n parseFortranNumber,\n formatFortranNumber,\n} from \"./fortran-helpers\";\n\nexport interface GTHConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as GTH.\n * Tabulated-only data cannot be inverted to analytical GTH form.\n /\nexport function canWriteGTH(pp: Pseudopotential): GTHConversionCheck {\n const reasons: string[] = [];\n if (!pp.gth) {\n reasons.push(\n \"no GTH analytical parameters (tabulated-only data cannot be inverted to GTH form)\",\n );\n }\n return { ok: reasons.length === 0, reasons };\n}\n\nexport interface GthParsedEntry {\n element: string;\n potentialName: string;\n aliases: string[];\n nElec: number[];\n rLoc: number;\n nexpPpl: number;\n cexpPpl: number[];\n nprj: number;\n channels: Array<{\n r: number;\n nprjPpnl: number;\n hprj: number[][];\n }>;\n hasKprj: boolean;\n kprj?: number[][][];\n}\n\n/* True for comment / blank / entry-boundary lines vs numeric data lines. /\nfunction isBoundaryLine(line: string \| undefined): boolean {\n if (line === undefined) return true;\n const t = line.trim();\n return t === \"\" \|\| t.startsWith(\"#\") \|\| !/^[-+.\\d]/.test(t);\n}\n\n/\n Expand upper-triangle values (row-major: h11, h12, ..., h1n, h22, ...)\n * into a full symmetric n×n matrix, matching GthData's [channel][i][j].\n /\nfunction upperToSymmetric(flat: number[], n: number): number[][] {\n const m: number[][] = [];\n for (let i = 0; i < n; i++) m.push(new Array(n).fill(0));\n let pos = 0;\n for (let i = 0; i < n; i++) {\n for (let j = i; j < n; j++) {\n const v = flat[pos++] ?? 0;\n m[i][j] = v;\n m[j][i] = v;\n }\n }\n return m;\n}\n\n/\n Parse a monolithic GTH_POTENTIALS file into individual element entries.\n /\nexport function parseGTHFile(text: string): GthParsedEntry[] {\n const entries: GthParsedEntry[] = [];\n const lines = text.split(\"\\n\");\n let i = 0;\n\n while (i < lines.length) {\n const line = lines[i].trim();\n\n // Skip comment lines and blank lines\n if (line.startsWith(\"#\") \|\| line === \"\") {\n i++;\n continue;\n }\n\n // This should be an element header line\n const headerParts = line.split(/\\s+/);\n if (headerParts.length < 2) {\n i++;\n continue;\n }\n\n const element = headerParts[0];\n const potentialName = headerParts[1] ?? \"\";\n const aliases = headerParts.slice(2);\n i++;\n\n // Skip comment lines between entries\n while (i < lines.length && (lines[i].trim().startsWith(\"#\") \|\| lines[i].trim() === \"\")) {\n i++;\n }\n\n if (i >= lines.length) break;\n\n // Valence electron configuration\n const nElec = lines[i++].trim().split(/\\s+/).map(Number);\n\n // Local part\n const localParts = lines[i++].trim().split(/\\s+/);\n const rLoc = parseFortranNumber(localParts[0]);\n const nexpPpl = parseInt(localParts[1]);\n const cexpPpl: number[] = [];\n for (let k = 0; k < nexpPpl; k++) {\n cexpPpl.push(parseFortranNumber(localParts[2 + k]));\n }\n\n // Number of non-local projector channels\n const nprj = parseInt(lines[i++].trim());\n\n // Non-local projector channels\n const channels: GthParsedEntry[\"channels\"] = [];\n let hasKprj = false;\n const kprjArrays: number[][][] = [];\n\n for (let l = 0; l < nprj && i < lines.length; l++) {\n const channelParts = lines[i++].trim().split(/\\s+/);\n const r = parseFortranNumber(channelParts[0]);\n const nprjPpnl = parseInt(channelParts[1]);\n\n // Upper-triangle size of the h-matrix for this channel.\n const hNeeded = (nprjPpnl (nprjPpnl + 1)) / 2;\n\n // Read h-matrix: inline tokens first, then one value per following line.\n const hFlat: number[] = [];\n let inlineIdx = 2;\n while (hFlat.length < hNeeded) {\n if (inlineIdx < channelParts.length) {\n hFlat.push(parseFortranNumber(channelParts[inlineIdx++]));\n } else if (i < lines.length) {\n hFlat.push(parseFortranNumber(lines[i++].trim().split(/\\s+/)[0]));\n } else {\n hFlat.push(0);\n }\n }\n const hprj: number[][] = upperToSymmetric(hFlat, nprjPpnl);\n\n channels.push({ r, nprjPpnl, hprj });\n\n // k-matrix (SOC): inline remainder on the channel line, if present.\n const inlineRemainder = channelParts.slice(inlineIdx).map(parseFortranNumber);\n if (\n !hasKprj &&\n inlineRemainder.length >= hNeeded &&\n inlineRemainder.every(Number.isFinite)\n ) {\n hasKprj = true;\n const kFlat = inlineRemainder.slice(0, hNeeded);\n const kmat = upperToSymmetric(kFlat, nprjPpnl);\n while (kprjArrays.length < l) kprjArrays.push([]);\n kprjArrays.push(kmat);\n } else if (!hasKprj && l === nprj - 1 && hNeeded > 0) {\n // Trailing multi-line k block: only valid on the LAST channel, where\n // the lines after it must be an entry boundary (not next-channel data).\n const kFlat: number[] = [];\n let j = i;\n while (kFlat.length < hNeeded && j < lines.length && !isBoundaryLine(lines[j])) {\n kFlat.push(parseFortranNumber(lines[j].trim().split(/\\s+/)[0]));\n j++;\n }\n if (kFlat.length === hNeeded && isBoundaryLine(lines[j])) {\n hasKprj = true;\n i = j;\n const kmat = upperToSymmetric(kFlat, nprjPpnl);\n while (kprjArrays.length < l) kprjArrays.push([]);\n kprjArrays.push(kmat);\n }\n }\n }\n\n entries.push({\n element,\n potentialName,\n aliases,\n nElec,\n rLoc,\n nexpPpl,\n cexpPpl,\n nprj,\n channels,\n hasKprj,\n kprj: hasKprj ? kprjArrays : undefined,\n });\n }\n\n return entries;\n}\n\n/*\n Evaluate the GTH local potential on a radial grid.\n \n V_local(r) = -Zval/r * erf(r / (sqrt(2) * r_loc))\n * + exp(-r²/(2r_loc²)) * (c0 + c1(r/r_loc)² + c2(r/r_loc)⁴ + c3(r/r_loc)⁶)\n \n * Units follow the units of cexpPpl (converted to Ry before calling).\n /\nfunction evalGthLocal(r: Float64Array, zVal: number, rLoc: number, cexpPpl: number[]): Float64Array {\n const vloc = new Float64Array(r.length);\n const c = [0, 0, 0, 0];\n for (let k = 0; k < cexpPpl.length && k < 4; k++) {\n c[k] = cexpPpl[k];\n }\n\n for (let i = 0; i < r.length; i++) {\n const ri = r[i];\n if (ri < 1e-15) {\n // At r=0, use L'Hopital: V_local(0) = -2Zval/(sqrt(2pi)rLoc) + c[0]\n vloc[i] = -2 * zVal / (Math.sqrt(2 * Math.PI) * rLoc) + c[0];\n continue;\n }\n\n const t = ri / rLoc;\n const t2 = t * t;\n const erfArg = ri / (Math.sqrt(2) * rLoc);\n const erfVal = erf(erfArg);\n const gauss = Math.exp(-t2 / 2);\n\n const coulomb = (-zVal / ri) * erfVal;\n const gaussian = gauss * (c[0] + c[1] * t2 + c[2] * t2 * t2 + c[3] * t2 * t2 * t2);\n\n vloc[i] = coulomb + gaussian;\n }\n\n return vloc;\n}\n\n/*\n Evaluate a GTH projector on a radial grid.\n \n \|r_{l,i}> = N * r^(l+2i-1) * exp(-r²/(2r_l²))\n /\nfunction evalGthProjector(\n r: Float64Array,\n l: number,\n i: number,\n rL: number,\n): Float64Array {\n const beta = new Float64Array(r.length);\n const exponent = l + 2 (i + 1) - 1;\n\n // Normalization constant\n const norm = Math.sqrt(2) * Math.pow(2 / (rL * rL), exponent + 0.5) /\n Math.sqrt(gamma(exponent + 0.5));\n\n for (let k = 0; k < r.length; k++) {\n const ri = r[k];\n if (ri < 1e-15) {\n beta[k] = exponent === 0 ? norm : 0;\n } else {\n beta[k] = norm * Math.pow(ri, exponent) * Math.exp(-ri * ri / (2 * rL * rL));\n }\n }\n\n return beta;\n}\n\n/*\n Parse a single GTH/HGH entry and convert to a first-class Pseudopotential.\n /\nexport function fromGTH(text: string): Pseudopotential {\n const entries = parseGTHFile(text);\n if (entries.length === 0) {\n throw new Error(\"No GTH entries found in file\");\n }\n return fromGthEntry(entries[0]);\n}\n\n/\n Parse a single GTH entry into a first-class Pseudopotential.\n \n Analytical parameters are converted to Ry and stored in `gth` alongside\n * an evaluated tabulation on a logarithmic grid.\n /\nexport function fromGthEntry(entry: GthParsedEntry): Pseudopotential {\n const zVal = entry.nElec.reduce((a, b) => a + b, 0);\n const lMax = entry.channels.length > 0 ? entry.channels.length - 1 : 0;\n\n const format: PseudopotentialFormat = /HGH/i.test(entry.potentialName)\n ? \"HGH\"\n : \"GTH\";\n\n // Build a logarithmic radial grid\n const npts = 500;\n const rmax = 20.0; // Bohr, sufficient for most pseudopotentials\n const { r, rab } = makeRadialGrid({ npts, rmax, type: \"log\" });\n\n // Convert analytical energies Hartree → Ry.\n const cexpPplRy = entry.cexpPpl.map(haToRy);\n const hprjRy = entry.channels.map((ch) =>\n ch.hprj.map((row) => row.map(haToRy)),\n );\n const kprjRy = entry.kprj?.map((m) => m.map((row) => row.map(haToRy)));\n\n // Evaluate local potential (Ry)\n const localVloc = evalGthLocal(r, zVal, entry.rLoc, cexpPplRy);\n\n // Evaluate projectors (normalization is unit-free)\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n\n for (let l = 0; l < entry.channels.length; l++) {\n const ch = entry.channels[l];\n for (let p = 0; p < ch.nprjPpnl; p++) {\n const betaData = evalGthProjector(r, l, p, ch.r);\n betas.push({\n index: projIdx + p,\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}${p + 1}`,\n beta: betaData,\n });\n }\n // D_ij is the full h-block: for GTH the h-matrix couples the\n // projectors of a channel directly.\n for (let p = 0; p < ch.nprjPpnl; p++) {\n for (let q = 0; q < ch.nprjPpnl; q++) {\n dij.push([projIdx + p, projIdx + q, hprjRy[l]?.[p]?.[q] ?? (p === q ? 1.0 : 0)]);\n }\n }\n projIdx += ch.nprjPpnl;\n }\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n rmax,\n r,\n rab,\n };\n\n // GTH analytical data (energies in Ry)\n const gthData: GthData = {\n nElec: entry.nElec,\n rLoc: entry.rLoc,\n cexpPpl: cexpPplRy,\n rPs: entry.channels.map((ch) => ch.r),\n hprj: hprjRy,\n kprj: kprjRy,\n };\n\n const header: PseudopotentialHeader = {\n element: entry.element,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: entry.hasKprj,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: false,\n functional: entry.potentialName,\n zValence: zVal,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: npts,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n };\n\n return {\n format,\n units: { ...CANONICAL_UNITS },\n provenance: {\n sourceFormat: format,\n analytical: true,\n notes:\n entry.aliases.length > 0 ? `aliases: ${entry.aliases.join(\", \")}` : undefined,\n },\n header,\n mesh,\n local: { vloc: localVloc } satisfies PseudopotentialLocal,\n nonlocal: { betas, dij } satisfies PseudopotentialNonlocal,\n pswfc: [],\n rhoatom: new Float64Array(npts),\n gth: gthData,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to GTH format (single element entry).\n * Analytical parameters are written back in Hartree (native GTH units);\n * the k-matrix is written inline on the channel line when present.\n /\nexport function toGTH(pp: Pseudopotential): string {\n const check = canWriteGTH(pp);\n if (!pp.gth) {\n throw new Error(check.reasons[0]);\n }\n\n const lines: string[] = [];\n const gth = pp.gth;\n\n lines.push(`# ${pp.header.element} ${pp.header.functional}`);\n lines.push(`# Element symbol Name of the potential Alias names`);\n lines.push(`# n_elec(s) n_elec(p) n_elec(d) ...`);\n lines.push(`# r_loc nexp_ppl cexp_ppl(1) ... cexp_ppl(nexp_ppl)`);\n lines.push(`# nprj`);\n lines.push(`${pp.header.element} ${pp.header.functional}`);\n\n // Valence electron configuration\n let nElec: number[];\n if (gth.nElec && gth.nElec.length > 0) {\n nElec = [...gth.nElec];\n } else {\n // Estimate from betas\n nElec = new Array(pp.header.lMax + 1).fill(0);\n for (const beta of pp.nonlocal.betas) {\n nElec[beta.angularMomentum] = Math.max(nElec[beta.angularMomentum], 1);\n }\n if (nElec[0] === 0) nElec[0] = Math.round(pp.header.zValence);\n }\n lines.push(nElec.join(\" \"));\n\n // Local part (Ry → Ha)\n const cHa = gth.cexpPpl.map((c) => c RY_TO_HA);\n lines.push(`${formatFortranNumber(gth.rLoc)} ${cHa.length} ${cHa.map((c) => formatFortranNumber(c)).join(\" \")}`);\n\n // Non-local part (Ry → Ha)\n lines.push(`${gth.rPs.length}`);\n for (let l = 0; l < gth.hprj.length; l++) {\n const h = gth.hprj[l];\n const nprj = h.length;\n // An empty padding entry (no k data for this channel) takes the legacy\n // layout; only channels with actual k values go inline.\n const k = gth.kprj?.[l];\n if (k && k.length > 0) {\n // k-matrix inline on the channel line so the parser recovers it.\n const hVals: string[] = [];\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n hVals.push(formatFortranNumber((h[i]?.[j] ?? 0) * RY_TO_HA));\n }\n }\n const kVals: string[] = [];\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n kVals.push(formatFortranNumber((k[i]?.[j] ?? 0) * RY_TO_HA));\n }\n }\n lines.push(\n `${formatFortranNumber(gth.rPs[l])} ${nprj} ${hVals.join(\" \")} ${kVals.join(\" \")}`,\n );\n } else {\n lines.push(`${formatFortranNumber(gth.rPs[l])} ${nprj}`);\n // h-matrix upper triangle\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n const val = (h[i]?.[j] ?? 0) * RY_TO_HA;\n lines.push(formatFortranNumber(val));\n }\n }\n }\n }\n\n return lines.join(\"\\n\");\n}\n\n// Simple error function approximation (Abramowitz & Stegun)\nfunction erf(x: number): number {\n const a1 = 0.254829592;\n const a2 = -0.284496736;\n const a3 = 1.421413741;\n const a4 = -1.453152027;\n const a5 = 1.061405429;\n const p = 0.3275911;\n\n const sign = x >= 0 ? 1 : -1;\n const absX = Math.abs(x);\n const t = 1.0 / (1.0 + p * absX);\n const y = 1.0 - (((((a5 * t + a4) * t) + a3) * t + a2) * t + a1) * t * Math.exp(-absX * absX);\n\n return sign * y;\n}\n\n// Gamma function approximation (Stirling + Lanczos for small arguments)\nfunction gamma(z: number): number {\n if (z < 0.5) {\n return Math.PI / (Math.sin(Math.PI * z) * gamma(1 - z));\n }\n z -= 1;\n const g = 7;\n const c = [\n 0.99999999999980993,\n 676.5203681218851,\n -1259.1392167224028,\n 771.32342877765313,\n -176.61502916214059,\n 12.507343278686905,\n -0.13857109526572012,\n 9.9843695780195716e-6,\n 1.5056327351493116e-7,\n ];\n let x = c[0];\n for (let i = 1; i < g + 2; i++) {\n x += c[i] / (z + i);\n }\n const t = z + g + 0.5;\n return Math.sqrt(2 * Math.PI) * Math.pow(t, z + 0.5) * Math.exp(-t) * x;\n}\n","/*\n Unified entry point for pseudopotential I/O.\n \n Every format adapter converts between text and the first-class\n * Pseudopotential object. This registry adds format detection plus\n * `parse` / `serialize` / `convert` dispatch so callers never need to know\n * which adapter to use.\n /\n\nimport type { Pseudopotential, PseudopotentialFormat } from \"../../pseudopotential/pseudopotential\";\n\nimport { fromUPF, toUPF } from \"./upf\";\nimport { fromUPFv1, toUPFv1 } from \"./upf-v1\";\nimport { fromPSP8, toPSP8, canWritePSP8 } from \"./psp8\";\nimport { fromPSML, toPSML, canWritePSML } from \"./psml\";\nimport { fromFHI, toFHI, canWriteFHI } from \"./fhi\";\nimport { fromGTH, toGTH, canWriteGTH } from \"./gth\";\n\n/* Non-empty lines of a text, for header sniffing. /\nfunction nonEmptyLines(text: string): string[] {\n return text.split(\"\\n\").filter((l) => l.trim().length > 0);\n}\n\n/\n Detect the pseudopotential format of a text buffer.\n \n Heuristics (first match wins):\n * - `<psml` tag → PSML\n * - `<UPF` root → UPF2\n * - `<PP_HEADER>` without `<UPF` → UPF1\n * - element + GTH/HGH header line → GTH\n * - pspcod=8 header line → PSP8\n * - FHI title / numeric lead → CPI (fromFHI auto-detects .fhi vs .cpi)\n \n @throws If no known format signature is found.\n /\nexport function detectFormat(text: string): PseudopotentialFormat {\n // Root-tag checks run on the file head only: these tags always open their\n // documents, and full-text regex scans dominate detection cost on\n // multi-MB PAW files.\n const head = text.slice(0, 4096);\n if (/<psml[\\s>]/i.test(head)) return \"PSML\";\n if (/<UPF[\\s>]/.test(head)) return \"UPF2\";\n if (/<PP_HEADER>/.test(head)) return \"UPF1\";\n\n const lines = nonEmptyLines(text);\n if (lines.length === 0) throw new Error(\"Cannot detect format of empty input\");\n\n // First content line (skipping #-comments, which lead GTH files and our\n // own serializer output).\n const content = lines.filter((l) => !l.trim().startsWith(\"#\"));\n const first = (content[0] ?? lines[0]).trim();\n if (/^[A-Z][a-z]?\\s+\\SHGH/i.test(first)) return \"HGH\";\n if (/^[A-Z][a-z]?\\s+\\S(GTH\|HGH)/i.test(first)) return \"GTH\";\n\n if (lines.length >= 3 && /^\\s8\\s+\\d+/.test(lines[2])) return \"PSP8\";\n\n if (\n /fhi98\|troullier\|martins\|pspdat/i.test(first) \|\|\n (/fhi/i.test(text.slice(0, 500)) && lines.length > 7 && /^\\s\\d/.test(lines[7] ?? \"\"))\n ) {\n return \"CPI\";\n }\n\n if (/^\\s[-+.\\d]/.test(first)) return \"CPI\";\n\n throw new Error(\"Unknown pseudopotential format: no recognized signature\");\n}\n\n/*\n Parse pseudopotential text into a first-class Pseudopotential object.\n * The format is auto-detected unless explicitly given.\n /\nexport function parse(\n text: string,\n format?: PseudopotentialFormat,\n): Pseudopotential {\n const fmt = format ?? detectFormat(text);\n switch (fmt) {\n case \"UPF2\":\n return fromUPF(text);\n case \"UPF1\":\n return fromUPFv1(text);\n case \"PSP8\":\n return fromPSP8(text);\n case \"PSML\":\n return fromPSML(text);\n case \"CPI\":\n return fromFHI(text);\n case \"GTH\":\n case \"HGH\":\n return fromGTH(text);\n default:\n throw new Error(`Unsupported pseudopotential format: ${fmt as string}`);\n }\n}\n\n/\n Serialize a first-class Pseudopotential to the requested format\n * (default UPF2, the lossless superset).\n /\nexport function serialize(\n pp: Pseudopotential,\n format: PseudopotentialFormat = \"UPF2\",\n): string {\n switch (format) {\n case \"UPF2\":\n return toUPF(pp);\n case \"UPF1\":\n return toUPFv1(pp);\n case \"PSP8\":\n return toPSP8(pp);\n case \"PSML\":\n return toPSML(pp);\n case \"CPI\":\n return toFHI(pp);\n case \"GTH\":\n case \"HGH\":\n return toGTH(pp);\n default:\n throw new Error(`Unsupported pseudopotential format: ${format as string}`);\n }\n}\n\n/\n Convert pseudopotential text from its (auto-detected) source format to a\n * target format. Lossy conversions (e.g. PAW → PSP8) produce best-effort\n * output; check `canSerialize()` first for safety.\n /\nexport function convert(\n text: string,\n target: PseudopotentialFormat,\n source?: PseudopotentialFormat,\n): string {\n return serialize(parse(text, source), target);\n}\n\nexport interface SerializationCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be faithfully written to\n * the requested format. UPF2 (the superset) is always safe.\n /\nexport function canSerialize(\n pp: Pseudopotential,\n format: PseudopotentialFormat,\n): SerializationCheck {\n switch (format) {\n case \"UPF2\":\n case \"UPF1\":\n return { ok: true, reasons: [] };\n case \"PSP8\":\n return canWritePSP8(pp);\n case \"PSML\":\n return canWritePSML(pp);\n case \"CPI\":\n return canWriteFHI(pp);\n case \"GTH\":\n case \"HGH\":\n return canWriteGTH(pp);\n default:\n return { ok: false, reasons: [`unknown format ${(format as string) ?? \"\"}`] };\n }\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\n/* Serializes a Structure to a JSON-serializable object. /\nexport function toJSON(structure: Structure) {\n return {\n lattice: Array.from(structure.lattice.basis.data),\n sites: structure.sites.map((s) => ({\n species: s.species,\n frac: Array.from(s.frac),\n })),\n };\n}\n\n/* Deserializes a Structure from a JSON object. /\nexport function fromJSON(data: any): Structure {\n return {\n lattice: createLattice(data.lattice),\n sites: data.sites.map((s: any) => ({\n species: s.species,\n frac: new Float64Array(s.frac),\n })),\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\nimport {\n AtomicNumberToSymbol,\n SymbolToAtomicNumber,\n} from \"@/core/data/periodictable\";\n\n/* A numpy-style serialized ndarray as produced by ASE's JSON encoder. /\ninterface ASEndarray {\n __ndarray__: [number[], string, Array<number \| boolean>];\n}\n\n/* An ASE `Atoms` object serialized through ase.io.jsonio.write_json. /\nexport interface ASEAtoms {\n numbers: ASEndarray;\n positions: ASEndarray;\n cell: ASEndarray;\n pbc: ASEndarray;\n __ase_objtype__: \"atoms\";\n [key: string]: unknown;\n}\n\nfunction decodeNdarray(obj: ASEndarray): Array<number \| boolean> {\n return obj.__ndarray__[2];\n}\n\nfunction encodeNdarray(\n shape: number[],\n dtype: string,\n data: Array<number \| boolean>,\n): ASEndarray {\n return { __ndarray__: [shape, dtype, data] };\n}\n\n/* Deserializes an ASE `Atoms` JSON object into a Structure.\n \n ASE stores Cartesian positions and atomic numbers; these are converted into\n * the library's fractional-coordinate representation using the supplied cell. /\nexport function fromASE(data: ASEAtoms): Structure {\n const cellFlat = decodeNdarray(data.cell) as number[];\n const lattice = createLattice(new Float64Array(cellFlat));\n\n const positions = decodeNdarray(data.positions) as number[];\n const numbers = decodeNdarray(data.numbers) as number[];\n\n const n = numbers.length;\n const sites = new Array(n);\n\n for (let i = 0; i < n; i++) {\n const z = numbers[i];\n const symbol = AtomicNumberToSymbol.get(z);\n\n if (symbol === undefined) {\n throw new Error(`Unknown atomic number ${z}`);\n }\n\n const cart = new Float64Array([\n positions[3 i],\n positions[3 * i + 1],\n positions[3 * i + 2],\n ]);\n\n const frac = fractional(lattice, cart);\n\n sites[i] = {\n species: { symbol },\n frac,\n };\n }\n\n const out: Structure & { pbc?: boolean[] } = { lattice, sites };\n\n const pbc = decodeNdarray(data.pbc) as boolean[];\n if (pbc.some((v) => !v)) {\n out.pbc = [pbc[0], pbc[1], pbc[2]];\n }\n\n return out;\n}\n\n/** Serializes a Structure to an ASE `Atoms` JSON object. /\nexport function toASE(structure: Structure): ASEAtoms {\n const m = structure.lattice.basis.data;\n\n const n = structure.sites.length;\n const positions = new Array<number>(n 3);\n const numbers = new Array<number>(n);\n\n for (let i = 0; i < n; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n positions[3 * i] = cart[0];\n positions[3 * i + 1] = cart[1];\n positions[3 * i + 2] = cart[2];\n\n const z = SymbolToAtomicNumber.get(site.species.symbol);\n\n if (z === undefined) {\n throw new Error(`Unknown element symbol ${site.species.symbol}`);\n }\n\n numbers[i] = z;\n }\n\n const pbc: boolean[] =\n (structure as Structure & { pbc?: boolean[] }).pbc ??\n [true, true, true];\n\n return {\n numbers: encodeNdarray([n], \"int64\", numbers),\n positions: encodeNdarray([n, 3], \"float64\", positions),\n cell: encodeNdarray([3, 3], \"float64\", Array.from(m)),\n pbc: encodeNdarray([3], \"bool\", pbc),\n __ase_objtype__: \"atoms\",\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\nimport { volume } from \"../lattice/volume\";\nimport { parameters } from \"../lattice/parameters\";\n\nimport { cartesian } from \"../site/cartesian\";\n\n/** A single pymatgen species entry (an element with occupancy). /\nexport interface PymatgenSpecies {\n element: string;\n occu: number;\n}\n\n/* A pymatgen lattice block. /\nexport interface PymatgenLattice {\n matrix: number[][];\n pbc?: boolean[];\n a?: number;\n b?: number;\n c?: number;\n alpha?: number;\n beta?: number;\n gamma?: number;\n volume?: number;\n [key: string]: unknown;\n}\n\n/* A pymatgen site block. /\nexport interface PymatgenSite {\n species: PymatgenSpecies[];\n abc: [number, number, number] \| number[];\n properties?: Record<string, unknown>;\n label?: string;\n xyz?: [number, number, number] \| number[];\n [key: string]: unknown;\n}\n\n/* A pymatgen `Structure` serialized via `Structure.to(fmt=\"json\")`. /\nexport interface PymatgenStructure {\n \"@module\": string;\n \"@class\": string;\n charge?: number;\n lattice: PymatgenLattice;\n properties?: Record<string, unknown>;\n sites: PymatgenSite[];\n [key: string]: unknown;\n}\n\nfunction flattenMatrix(matrix: number[][]): number[] {\n const out: number[] = [];\n\n for (const row of matrix) {\n for (const v of row) {\n out.push(v);\n }\n }\n\n return out;\n}\n\n/* Deserializes a pymatgen `Structure` JSON object into a Structure. /\nexport function fromPymatgen(data: PymatgenStructure): Structure {\n const lattice = createLattice(new Float64Array(flattenMatrix(data.lattice.matrix)));\n\n const sites = data.sites.map((site) => {\n const primary = site.species[0];\n\n if (primary === undefined) {\n throw new Error(\"Site has no species\");\n }\n\n const label = site.label ?? primary.element;\n\n return {\n species: {\n symbol: primary.element,\n properties: { occu: primary.occu, label },\n },\n\n frac: new Float64Array(site.abc),\n };\n });\n\n const out: Structure & { charge?: number; properties?: unknown } = {\n lattice,\n sites,\n };\n\n if (data.charge !== undefined) {\n out.charge = data.charge;\n }\n\n if (data.properties !== undefined) {\n out.properties = data.properties;\n }\n\n return out;\n}\n\n/* Serializes a Structure to a pymatgen `Structure` JSON object. /\nexport function toPymatgen(structure: Structure): PymatgenStructure {\n const m = structure.lattice.basis.data;\n\n const matrix = [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ];\n\n const [a, b, c, alpha, beta, gamma] = parameters(structure.lattice);\n\n const sites = structure.sites.map((site) => {\n const props = site.species.properties ?? {};\n\n const label = (props.label as string) ?? site.species.symbol;\n const occu = (props.occu as number) ?? 1;\n\n const cart = cartesian(structure.lattice, site);\n\n return {\n species: [{ element: site.species.symbol, occu }],\n abc: Array.from(site.frac),\n properties: {},\n label,\n xyz: Array.from(cart),\n };\n });\n\n return {\n \"@module\": \"pymatgen.core.structure\",\n \"@class\": \"Structure\",\n charge: (structure as Structure & { charge?: number }).charge ?? 0.0,\n lattice: {\n matrix,\n pbc: [true, true, true],\n a,\n b,\n c,\n alpha,\n beta,\n gamma,\n volume: volume(structure.lattice),\n },\n properties:\n (structure as Structure & { properties?: Record<string, unknown> })\n .properties ?? {},\n sites,\n };\n}\n","/\n Validation for first-class pseudopotential objects.\n \n `validate()` returns a list of human-readable issues (empty = valid).\n * Structural mismatches (wrong array lengths, out-of-range D_ij indices) are\n * the main target; physical sanity (signs, cutoffs) is reported as warnings\n * with a \"warn:\" prefix.\n /\n\nimport type { Pseudopotential } from \"./pseudopotential\";\n\n/* Validate a pseudopotential object, returning a list of issue strings. /\nexport function validate(pp: Pseudopotential): string[] {\n const issues: string[] = [];\n const n = pp.mesh.r.length;\n\n if (n === 0) issues.push(\"mesh.r is empty\");\n if (pp.mesh.rab.length !== n) {\n issues.push(\n `mesh.rab length ${pp.mesh.rab.length} != mesh.r length ${n}`,\n );\n }\n if (pp.header.meshSize !== n) {\n issues.push(\n `header.meshSize ${pp.header.meshSize} != mesh.r length ${n}`,\n );\n }\n if (pp.local.vloc.length !== n) {\n issues.push(`local.vloc length ${pp.local.vloc.length} != mesh size ${n}`);\n }\n if (pp.rhoatom.length !== 0 && pp.rhoatom.length !== n) {\n issues.push(`rhoatom length ${pp.rhoatom.length} != mesh size ${n}`);\n }\n if (pp.nlcc && pp.nlcc.length !== n) {\n issues.push(`nlcc length ${pp.nlcc.length} != mesh size ${n}`);\n }\n\n const nBetas = pp.nonlocal.betas.length;\n if (pp.header.numberOfProj !== 0 && pp.header.numberOfProj !== nBetas) {\n issues.push(\n `header.numberOfProj ${pp.header.numberOfProj} != betas length ${nBetas}`,\n );\n }\n pp.nonlocal.betas.forEach((beta, i) => {\n if (beta.beta.length !== n) {\n issues.push(\n `beta[${i}] (l=${beta.angularMomentum}) length ${beta.beta.length} != mesh size ${n}`,\n );\n }\n });\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n if (!Number.isInteger(nb) \|\| nb < 1 \|\| nb > nBetas) {\n issues.push(`dij entry [${nb}, ${mb}] has out-of-range nb=${nb}`);\n }\n if (!Number.isInteger(mb) \|\| mb < 1 \|\| mb > nBetas) {\n issues.push(`dij entry [${nb}, ${mb}] has out-of-range mb=${mb}`);\n }\n if (Number.isNaN(val)) issues.push(`dij entry [${nb}, ${mb}] is NaN`);\n }\n\n if (pp.header.numberOfWfc !== 0 && pp.header.numberOfWfc !== pp.pswfc.length) {\n issues.push(\n `header.numberOfWfc ${pp.header.numberOfWfc} != pswfc length ${pp.pswfc.length}`,\n );\n }\n pp.pswfc.forEach((wfc, i) => {\n if (wfc.chi.length !== n) {\n issues.push(`pswfc[${i}] chi length ${wfc.chi.length} != mesh size ${n}`);\n }\n });\n if (pp.semilocal) {\n pp.semilocal.forEach((sl, i) => {\n if (sl.vnl.length !== n) {\n issues.push(\n `semilocal[${i}] (l=${sl.l}) length ${sl.vnl.length} != mesh size ${n}`,\n );\n }\n });\n }\n if (pp.fullWfc) {\n pp.fullWfc.forEach((wfc, i) => {\n if (wfc.aewfc.length !== n) {\n issues.push(\n `fullWfc[${i}] aewfc length ${wfc.aewfc.length} != mesh size ${n}`,\n );\n }\n });\n }\n\n const aug = pp.nonlocal.augmentation;\n if (aug) {\n if (aug.q && aug.q.length === 0) issues.push(\"augmentation.q is empty\");\n if (aug.qijl) {\n aug.qijl.forEach((q, i) => {\n if (q.qijl.length !== n) {\n issues.push(\n `augmentation.qijl[${i}] (i=${q.i},j=${q.j},l=${q.l}) length ${q.qijl.length} != mesh size ${n}`,\n );\n }\n if (q.i < 1 \|\| q.i > nBetas \|\| q.j < 1 \|\| q.j > nBetas) {\n issues.push(\n `augmentation.qijl[${i}] references out-of-range projectors (i=${q.i},j=${q.j})`,\n );\n }\n });\n }\n }\n\n if (pp.paw) {\n if (pp.paw.aeVloc.length !== 0 && pp.paw.aeVloc.length !== n) {\n issues.push(`paw.aeVloc length ${pp.paw.aeVloc.length} != mesh size ${n}`);\n }\n if (pp.paw.aeNlcc.length !== 0 && pp.paw.aeNlcc.length !== n) {\n issues.push(`paw.aeNlcc length ${pp.paw.aeNlcc.length} != mesh size ${n}`);\n }\n }\n\n if (pp.units.energy !== \"Ry\" \|\| pp.units.length !== \"Bohr\") {\n issues.push(\n `warn: non-canonical units energy=${pp.units.energy} length=${pp.units.length}`,\n );\n }\n if (pp.header.isPaw && !pp.paw) {\n issues.push(\"warn: header.isPaw is set but paw data is missing\");\n }\n if (pp.header.hasSo && !pp.spinOrbit) {\n issues.push(\"warn: header.hasSo is set but spinOrbit data is missing\");\n }\n\n return issues;\n}\n","/\n Maps each International spacegroup number (1-230) to the list of possible\n * Hall numbers for that spacegroup.\n \n Source: Seto's Home Page\n * http://pmsl.planet.sci.kobe-u.ac.jp/~seto/?page_id=37&lang=en\n /\nexport const hallNumbersOfSpacegroup: Record<number, number[]> = {\n 1: [1],\n 2: [2],\n 3: [3, 4, 5],\n 4: [6, 7, 8],\n 5: [9, 10, 11, 12, 13, 14, 15, 16, 17],\n 6: [18, 19, 20],\n 7: [21, 22, 23, 24, 25, 26, 27, 28, 29],\n 8: [30, 31, 32, 33, 34, 35, 36, 37, 38],\n 9: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56],\n 10: [57, 58, 59],\n 11: [60, 61, 62],\n 12: [63, 64, 65, 66, 67, 68, 69, 70, 71],\n 13: [72, 73, 74, 75, 76, 77, 78, 79, 80],\n 14: [81, 82, 83, 84, 85, 86, 87, 88, 89],\n 15: [\n 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,\n 107,\n ],\n 16: [108],\n 17: [109, 110, 111],\n 18: [112, 113, 114],\n 19: [115],\n 20: [116, 117, 118],\n 21: [119, 120, 121],\n 22: [122],\n 23: [123],\n 24: [124],\n 25: [125, 126, 127],\n 26: [128, 129, 130, 131, 132, 133],\n 27: [134, 135, 136],\n 28: [137, 138, 139, 140, 141, 142],\n 29: [143, 144, 145, 146, 147, 148],\n 30: [149, 150, 151, 152, 153, 154],\n 31: [155, 156, 157, 158, 159, 160],\n 32: [161, 162, 163],\n 33: [164, 165, 166, 167, 168, 169],\n 34: [170, 171, 172],\n 35: [173, 174, 175],\n 36: [176, 177, 178, 179, 180, 181],\n 37: [182, 183, 184],\n 38: [185, 186, 187, 188, 189, 190],\n 39: [191, 192, 193, 194, 195, 196],\n 40: [197, 198, 199, 200, 201, 202],\n 41: [203, 204, 205, 206, 207, 208],\n 42: [209, 210, 211],\n 43: [212, 213, 214],\n 44: [215, 216, 217],\n 45: [218, 219, 220],\n 46: [221, 222, 223, 224, 225, 226],\n 47: [227],\n 48: [228, 229],\n 49: [230, 231, 232],\n 50: [233, 234, 235, 236, 237, 238],\n 51: [239, 240, 241, 242, 243, 244],\n 52: [245, 246, 247, 248, 249, 250],\n 53: [251, 252, 253, 254, 255, 256],\n 54: [257, 258, 259, 260, 261, 262],\n 55: [263, 264, 265],\n 56: [266, 267, 268],\n 57: [269, 270, 271, 272, 273, 274],\n 58: [275, 276, 277],\n 59: [278, 279, 280, 281, 282, 283],\n 60: [284, 285, 286, 287, 288, 289],\n 61: [290, 291],\n 62: [292, 293, 294, 295, 296, 297],\n 63: [298, 299, 300, 301, 302, 303],\n 64: [304, 305, 306, 307, 308, 309],\n 65: [310, 311, 312],\n 66: [313, 314, 315],\n 67: [316, 317, 318, 319, 320, 321],\n 68: [322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333],\n 69: [334],\n 70: [335, 336],\n 71: [337],\n 72: [338, 339, 340],\n 73: [341, 342],\n 74: [343, 344, 345, 346, 347, 348],\n 75: [349],\n 76: [350],\n 77: [351],\n 78: [352],\n 79: [353],\n 80: [354],\n 81: [355],\n 82: [356],\n 83: [357],\n 84: [358],\n 85: [359, 360],\n 86: [361, 362],\n 87: [363],\n 88: [364, 365],\n 89: [366],\n 90: [367],\n 91: [368],\n 92: [369],\n 93: [370],\n 94: [371],\n 95: [372],\n 96: [373],\n 97: [374],\n 98: [375],\n 99: [376],\n 100: [377],\n 101: [378],\n 102: [379],\n 103: [380],\n 104: [381],\n 105: [382],\n 106: [383],\n 107: [384],\n 108: [385],\n 109: [386],\n 110: [387],\n 111: [388],\n 112: [389],\n 113: [390],\n 114: [391],\n 115: [392],\n 116: [393],\n 117: [394],\n 118: [395],\n 119: [396],\n 120: [397],\n 121: [398],\n 122: [399],\n 123: [400],\n 124: [401],\n 125: [402, 403],\n 126: [404, 405],\n 127: [406],\n 128: [407],\n 129: [408, 409],\n 130: [410, 411],\n 131: [412],\n 132: [413],\n 133: [414, 415],\n 134: [416, 417],\n 135: [418],\n 136: [419],\n 137: [420, 421],\n 138: [422, 423],\n 139: [424],\n 140: [425],\n 141: [426, 427],\n 142: [428, 429],\n 143: [430],\n 144: [431],\n 145: [432],\n 146: [433, 434],\n 147: [435],\n 148: [436, 437],\n 149: [438],\n 150: [439],\n 151: [440],\n 152: [441],\n 153: [442],\n 154: [443],\n 155: [444, 445],\n 156: [446],\n 157: [447],\n 158: [448],\n 159: [449],\n 160: [450, 451],\n 161: [452, 453],\n 162: [454],\n 163: [455],\n 164: [456],\n 165: [457],\n 166: [458, 459],\n 167: [460, 461],\n 168: [462],\n 169: [463],\n 170: [464],\n 171: [465],\n 172: [466],\n 173: [467],\n 174: [468],\n 175: [469],\n 176: [470],\n 177: [471],\n 178: [472],\n 179: [473],\n 180: [474],\n 181: [475],\n 182: [476],\n 183: [477],\n 184: [478],\n 185: [479],\n 186: [480],\n 187: [481],\n 188: [482],\n 189: [483],\n 190: [484],\n 191: [485],\n 192: [486],\n 193: [487],\n 194: [488],\n 195: [489],\n 196: [490],\n 197: [491],\n 198: [492],\n 199: [493],\n 200: [494],\n 201: [495, 496],\n 202: [497],\n 203: [498, 499],\n 204: [500],\n 205: [501],\n 206: [502],\n 207: [503],\n 208: [504],\n 209: [505],\n 210: [506],\n 211: [507],\n 212: [508],\n 213: [509],\n 214: [510],\n 215: [511],\n 216: [512],\n 217: [513],\n 218: [514],\n 219: [515],\n 220: [516],\n 221: [517],\n 222: [518, 519],\n 223: [520],\n 224: [521, 522],\n 225: [523],\n 226: [524],\n 227: [525, 526],\n 228: [527, 528],\n 229: [529],\n 230: [530],\n};\n","/\n Point group data: mapping, character tables, symmetry operations, and\n * optical activity labels for all 27 non-cubic crystallographic point groups.\n \n Rotation matrices are generated at runtime from axis/angle specs via\n * quaternion rotation (matching the Python/ASE Quaternion implementation).\n /\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport type Vec3 = [number, number, number];\nexport type Matrix3x3 = [Vec3, Vec3, Vec3];\n/* Complex number as [real, imaginary]. /\nexport type Complex = [number, number];\n\n// Symmetry operation specs — declarative, not pre-computed\ninterface IdentityOp {\n type: \"I\";\n}\ninterface InversionOp {\n type: \"-I\";\n}\ninterface RotationOp {\n type: \"R\";\n axis: Vec3;\n angle: number;\n}\ninterface RotoreflectionOp {\n type: \"S\";\n axis: Vec3;\n angle: number;\n}\nexport type OpSpec = IdentityOp \| InversionOp \| RotationOp \| RotoreflectionOp;\n\nexport interface PointGroupEntry {\n classes: Record<number, OpSpec[]>;\n characterTable: Record<string, (number \| Complex)[]>;\n raman: string[];\n infrared: string[];\n hmSymbol: string;\n backscattering: string[][];\n}\n\n// ---------------------------------------------------------------------------\n// Matrix generation from OpSpec\n// ---------------------------------------------------------------------------\n\nconst TOL = 2 Number.EPSILON;\n\nexport function identity(): Matrix3x3 {\n return [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ];\n}\n\nexport function inversion(): Matrix3x3 {\n return [\n [-1, 0, 0],\n [0, -1, 0],\n [0, 0, -1],\n ];\n}\n\n/*\n Rotation matrix from axis and angle via quaternion.\n * Equivalent to ASE's Quaternion.rotation_matrix().\n /\nexport function rotationMatrix(axis: Vec3, angle: number): Matrix3x3 {\n const [ax, ay, az] = axis;\n const norm = Math.sqrt(ax ax + ay * ay + az * az);\n const half = angle / 2;\n const s = Math.sin(half) / norm;\n const c = Math.cos(half);\n // Quaternion [w, x, y, z]\n const qw = c;\n const qx = s * ax;\n const qy = s * ay;\n const qz = s * az;\n\n const raw: number[][] = [\n [\n 1 - 2 * (qy * qy + qz * qz),\n 2 * (qx * qy - qw * qz),\n 2 * (qx * qz + qw * qy),\n ],\n [\n 2 * (qx * qy + qw * qz),\n 1 - 2 * (qx * qx + qz * qz),\n 2 * (qy * qz - qw * qx),\n ],\n [\n 2 * (qx * qz - qw * qy),\n 2 * (qy * qz + qw * qx),\n 1 - 2 * (qx * qx + qy * qy),\n ],\n ];\n\n // Zero out near-zero entries (matches Python's tolerance logic)\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n if (Math.abs(raw[i][j]) < TOL) raw[i][j] = 0;\n }\n }\n\n return raw as Matrix3x3;\n}\n\n/*\n Rotoreflection: rotation by angle + π, then negate (inversion).\n * Equivalent to Python's `rotoreflection(axis, angle) = -rotation(axis, angle + π)`.\n /\nexport function rotoreflectionMatrix(axis: Vec3, angle: number): Matrix3x3 {\n const m = rotationMatrix(axis, angle + Math.PI);\n return [\n [-m[0][0], -m[0][1], -m[0][2]],\n [-m[1][0], -m[1][1], -m[1][2]],\n [-m[2][0], -m[2][1], -m[2][2]],\n ];\n}\n\n/* Resolve an OpSpec to its concrete 3×3 matrix. /\nexport function resolveOp(op: OpSpec): Matrix3x3 {\n switch (op.type) {\n case \"I\":\n return identity();\n case \"-I\":\n return inversion();\n case \"R\":\n return rotationMatrix(op.axis, op.angle);\n case \"S\":\n return rotoreflectionMatrix(op.axis, op.angle);\n }\n}\n\n/* Resolve all operations in a class to their matrices. /\nexport function resolveClass(ops: OpSpec[]): Matrix3x3[] {\n return ops.map(resolveOp);\n}\n\n// ---------------------------------------------------------------------------\n// Common shorthand specs\n// ---------------------------------------------------------------------------\n\nconst I: IdentityOp = { type: \"I\" };\nconst NI: InversionOp = { type: \"-I\" };\n\nconst rz = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [0, 0, 1],\n angle,\n});\nconst rx = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [1, 0, 0],\n angle,\n});\nconst ry = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [0, 1, 0],\n angle,\n});\nconst rAxis = (axis: Vec3, angle: number): RotationOp => ({\n type: \"R\",\n axis,\n angle,\n});\n\nconst sx = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [1, 0, 0],\n angle,\n});\nconst sy = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [0, 1, 0],\n angle,\n});\nconst sz = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [0, 0, 1],\n angle,\n});\nconst sAxis = (axis: Vec3, angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis,\n angle,\n});\n\n// Frequently used irrational-containing axes\nconst SQRT3 = Math.sqrt(3);\nconst AX_N1_SQ3_0: Vec3 = [-1, SQRT3, 0];\nconst AX_N1_NSQ3_0: Vec3 = [-1, -SQRT3, 0];\nconst AX_SQ3_1_0: Vec3 = [SQRT3, 1, 0];\nconst AX_SQ3_N1_0: Vec3 = [SQRT3, -1, 0];\nconst AX_1_1_0: Vec3 = [1, 1, 0];\nconst AX_1_N1_0: Vec3 = [1, -1, 0];\n\n// Common angles\nconst PI = Math.PI;\nconst PI2 = PI / 2;\nconst PI3 = PI / 3;\nconst PI6 = PI / 6;\nconst TPI3 = (2 PI) / 3;\nconst NTPI3 = -(2 * PI) / 3;\nconst NPI3 = -PI / 3;\n\n// ---------------------------------------------------------------------------\n// Complex number constants (character table phase factors)\n// ---------------------------------------------------------------------------\n\n// w = exp(2πi/3), w2 = exp(-2πi/3)\nconst W: Complex = [-0.5, SQRT3 / 2];\nconst W2: Complex = [-0.5, -SQRT3 / 2];\nconst _1j: Complex = [0, 1];\nconst _1nj: Complex = [0, -1];\n\n// ---------------------------------------------------------------------------\n// International number ↔ HM/Schoenflies mapping\n// ---------------------------------------------------------------------------\n\nexport interface PGMapping {\n internationalNumber: number;\n hmSymbol: string;\n schoenflies: string;\n}\n\nexport const pointgroupMapping: PGMapping[] = [\n { internationalNumber: 0, hmSymbol: \"\", schoenflies: \"\" }, // placeholder for 1-indexing\n { internationalNumber: 1, hmSymbol: \"1\", schoenflies: \"C1\" },\n { internationalNumber: 2, hmSymbol: \"-1\", schoenflies: \"Ci\" },\n { internationalNumber: 3, hmSymbol: \"2\", schoenflies: \"C2\" },\n { internationalNumber: 4, hmSymbol: \"m\", schoenflies: \"Cs\" },\n { internationalNumber: 5, hmSymbol: \"2/m\", schoenflies: \"C2h\" },\n { internationalNumber: 6, hmSymbol: \"222\", schoenflies: \"D2\" },\n { internationalNumber: 7, hmSymbol: \"mm2\", schoenflies: \"C2v\" },\n { internationalNumber: 8, hmSymbol: \"mmm\", schoenflies: \"D2h\" },\n { internationalNumber: 9, hmSymbol: \"4\", schoenflies: \"C4\" },\n { internationalNumber: 10, hmSymbol: \"-4\", schoenflies: \"S4\" },\n { internationalNumber: 11, hmSymbol: \"4/m\", schoenflies: \"C4h\" },\n { internationalNumber: 12, hmSymbol: \"422\", schoenflies: \"D4\" },\n { internationalNumber: 13, hmSymbol: \"4mm\", schoenflies: \"C4v\" },\n { internationalNumber: 14, hmSymbol: \"-42m\", schoenflies: \"D2d\" },\n { internationalNumber: 15, hmSymbol: \"4/mmm\", schoenflies: \"D4h\" },\n { internationalNumber: 16, hmSymbol: \"3\", schoenflies: \"C3\" },\n { internationalNumber: 17, hmSymbol: \"-3\", schoenflies: \"C3i\" },\n { internationalNumber: 18, hmSymbol: \"32\", schoenflies: \"D3\" },\n { internationalNumber: 19, hmSymbol: \"3m\", schoenflies: \"C3v\" },\n { internationalNumber: 20, hmSymbol: \"-3m\", schoenflies: \"D3d\" },\n { internationalNumber: 21, hmSymbol: \"6\", schoenflies: \"C6\" },\n { internationalNumber: 22, hmSymbol: \"-6\", schoenflies: \"C3h\" },\n { internationalNumber: 23, hmSymbol: \"6/m\", schoenflies: \"C6h\" },\n { internationalNumber: 24, hmSymbol: \"622\", schoenflies: \"D6\" },\n { internationalNumber: 25, hmSymbol: \"6mm\", schoenflies: \"C6v\" },\n { internationalNumber: 26, hmSymbol: \"-6m2\", schoenflies: \"D3h\" },\n { internationalNumber: 27, hmSymbol: \"6/mmm\", schoenflies: \"D6h\" },\n // Cubic (kept for completeness, not used in layer analysis)\n { internationalNumber: 28, hmSymbol: \"23\", schoenflies: \"T\" },\n { internationalNumber: 29, hmSymbol: \"m-3\", schoenflies: \"Th\" },\n { internationalNumber: 30, hmSymbol: \"432\", schoenflies: \"O\" },\n { internationalNumber: 31, hmSymbol: \"-43m\", schoenflies: \"Td\" },\n { internationalNumber: 32, hmSymbol: \"m-3m\", schoenflies: \"Oh\" },\n];\n\n// ---------------------------------------------------------------------------\n// Point group dictionary — all 27 non-cubic groups\n// ---------------------------------------------------------------------------\n\nexport const pointgroupDict: Record<string, PointGroupEntry> = {\n // =======================================================================\n // TRICLINIC\n // =======================================================================\n\n C1: {\n classes: { 0: [I] },\n characterTable: { A: [1] },\n raman: [\"A\"],\n infrared: [\"A\"],\n hmSymbol: \"1\",\n backscattering: [[\"A\"], [\"A\"], [\"A\"]],\n },\n\n Ci: {\n classes: { 0: [I], 1: [NI] },\n characterTable: { Ag: [1, 1], Au: [1, -1] },\n raman: [\"Ag\"],\n infrared: [\"Au\"],\n hmSymbol: \"-1\",\n backscattering: [[\"Ag\"], [\"Ag\"], [\"Ag\"]],\n },\n\n // =======================================================================\n // MONOCLINIC\n // =======================================================================\n\n C2: {\n classes: { 0: [I], 1: [rz(PI)] },\n characterTable: { A: [1, 1], B: [1, -1] },\n raman: [\"A\", \"B\"],\n infrared: [\"A\", \"B\"],\n hmSymbol: \"2\",\n backscattering: [[\"A\", \"B\"], [\"A\", \"B\"], [\"A\"]],\n },\n\n Cs: {\n classes: { 0: [I], 1: [sz(0)] },\n characterTable: { \"A'\": [1, 1], \"A''\": [1, -1] },\n raman: [\"A'\", \"A''\"],\n infrared: [\"A'\", \"A''\"],\n hmSymbol: \"m\",\n backscattering: [[\"A'\", \"A''\"], [\"A'\", \"A''\"], [\"A'\"]],\n },\n\n C2h: {\n classes: { 0: [I], 1: [rz(PI)], 2: [NI], 3: [sz(0)] },\n characterTable: {\n Ag: [1, 1, 1, 1],\n Bg: [1, -1, 1, -1],\n Au: [1, 1, -1, -1],\n Bu: [1, -1, -1, 1],\n },\n raman: [\"Ag\", \"Bg\"],\n infrared: [\"Au\", \"Bu\"],\n hmSymbol: \"2/m\",\n backscattering: [[\"Ag\", \"Bg\"], [\"Ag\", \"Bg\"], [\"Ag\"]],\n },\n\n // =======================================================================\n // ORTHORHOMBIC\n // =======================================================================\n\n D2: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [ry(PI)],\n 3: [rx(PI)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B1: [1, 1, -1, -1],\n B2: [1, -1, 1, -1],\n B3: [1, -1, -1, 1],\n },\n raman: [\"A\", \"B1\", \"B2\", \"B3\"],\n infrared: [\"B1\", \"B2\", \"B3\"],\n hmSymbol: \"222\",\n backscattering: [\n [\"A\", \"B3\"],\n [\"A\", \"B2\"],\n [\"A\", \"B1\"],\n ],\n },\n\n C2v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sy(0)],\n 3: [sx(0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1],\n A2: [1, 1, -1, -1],\n B1: [1, -1, 1, -1],\n B2: [1, -1, -1, 1],\n },\n raman: [\"A1\", \"A2\", \"B1\", \"B2\"],\n infrared: [\"A1\", \"B1\", \"B2\"],\n hmSymbol: \"mm2\",\n backscattering: [\n [\"A1\", \"B2\"],\n [\"A1\", \"B1\"],\n [\"A1\", \"A2\"],\n ],\n },\n\n D2h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [ry(PI)],\n 3: [rx(PI)],\n 4: [NI],\n 5: [sz(0)],\n 6: [sy(0)],\n 7: [sx(0)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1],\n B1g: [1, 1, -1, -1, 1, 1, -1, -1],\n B2g: [1, -1, 1, -1, 1, -1, 1, -1],\n B3g: [1, -1, -1, 1, 1, -1, -1, 1],\n Au: [1, 1, 1, 1, -1, -1, -1, -1],\n B1u: [1, 1, -1, -1, -1, -1, 1, 1],\n B2u: [1, -1, 1, -1, -1, 1, -1, 1],\n B3u: [1, -1, -1, 1, -1, 1, 1, -1],\n },\n raman: [\"Ag\", \"B1g\", \"B2g\", \"B3g\"],\n infrared: [\"B1u\", \"B2u\", \"B3u\"],\n hmSymbol: \"mmm\",\n backscattering: [\n [\"Ag\", \"B3g\"],\n [\"Ag\", \"B2g\"],\n [\"Ag\", \"B1g\"],\n ],\n },\n\n // =======================================================================\n // TETRAGONAL\n // =======================================================================\n\n C4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2)],\n 3: [rz(-PI2)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B: [1, 1, -1, -1],\n \"1E\": [1, -1, _1nj, _1j],\n \"2E\": [1, -1, _1j, _1nj],\n },\n raman: [\"A\", \"B\", \"1E\", \"2E\"],\n infrared: [\"A\", \"1E\", \"2E\"],\n hmSymbol: \"4\",\n backscattering: [\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"B\"],\n ],\n },\n\n S4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sz(PI2)],\n 3: [sz(-PI2)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B: [1, 1, -1, -1],\n \"1E\": [1, -1, _1nj, _1j],\n \"2E\": [1, -1, _1j, _1nj],\n },\n raman: [\"A\", \"B\", \"1E\", \"2E\"],\n infrared: [\"B\", \"1E\", \"2E\"],\n hmSymbol: \"-4\",\n backscattering: [\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"B\"],\n ],\n },\n\n C4h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2)],\n 3: [rz(-PI2)],\n 4: [NI],\n 5: [sz(0)],\n 6: [sz(-PI2)],\n 7: [sz(PI2)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1],\n Bg: [1, 1, -1, -1, 1, 1, -1, -1],\n \"1Eg\": [1, -1, _1nj, _1j, 1, -1, _1nj, _1j],\n \"2Eg\": [1, -1, _1j, _1nj, 1, -1, _1j, _1nj],\n Au: [1, 1, 1, 1, -1, -1, -1, -1],\n Bu: [1, 1, -1, -1, -1, -1, 1, 1],\n \"1Eu\": [1, -1, _1nj, _1j, -1, 1, _1j, _1nj],\n \"2Eu\": [1, -1, _1j, _1nj, -1, 1, _1nj, _1j],\n },\n raman: [\"Ag\", \"Bg\", \"1Eg\", \"2Eg\"],\n infrared: [\"Au\", \"1Eu\", \"2Eu\"],\n hmSymbol: \"4/m\",\n backscattering: [\n [\"Ag\", \"1Eg\", \"2Eg\", \"Bg\"],\n [\"Ag\", \"1Eg\", \"2Eg\", \"Bg\"],\n [\"Ag\", \"Bg\"],\n ],\n },\n\n D4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [rAxis(AX_1_1_0, PI), rAxis(AX_1_N1_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"A2\", \"E\"],\n hmSymbol: \"422\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n C4v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [sx(0), sy(0)],\n 4: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"A1\", \"E\"],\n hmSymbol: \"4mm\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n D2d: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sz(PI2), sz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"B2\", \"E\"],\n hmSymbol: \"-42m\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n D4h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [rAxis(AX_1_1_0, PI), rAxis(AX_1_N1_0, PI)],\n 5: [NI],\n 6: [sz(0)],\n 7: [sz(PI2), sz(-PI2)],\n 8: [sx(0), sy(0)],\n 9: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n A2g: [1, 1, 1, -1, -1, 1, 1, 1, -1, -1],\n B1g: [1, 1, -1, 1, -1, 1, 1, -1, 1, -1],\n B2g: [1, 1, -1, -1, 1, 1, 1, -1, -1, 1],\n Eg: [2, -2, 0, 0, 0, 2, -2, 0, 0, 0],\n A1u: [1, 1, 1, 1, 1, -1, -1, -1, -1, -1],\n A2u: [1, 1, 1, -1, -1, -1, -1, -1, 1, 1],\n B1u: [1, 1, -1, 1, -1, -1, -1, 1, -1, 1],\n B2u: [1, 1, -1, -1, 1, -1, -1, 1, 1, -1],\n Eu: [2, -2, 0, 0, 0, -2, 2, 0, 0, 0],\n },\n raman: [\"A1g\", \"B1g\", \"B2g\", \"Eg\"],\n infrared: [\"A2u\", \"Eu\"],\n hmSymbol: \"4/mmm\",\n backscattering: [\n [\"A1g\", \"Eg\", \"B1g\"],\n [\"A1g\", \"Eg\", \"B1g\"],\n [\"A1g\", \"B1g\", \"B2g\"],\n ],\n },\n\n // =======================================================================\n // TRIGONAL\n // =======================================================================\n\n C3: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n },\n characterTable: {\n A: [1, 1, 1],\n \"1E\": [1, W2, W],\n \"2E\": [1, W, W2],\n },\n raman: [\"A\", \"1E\", \"2E\"],\n infrared: [\"A\", \"1E\", \"2E\"],\n hmSymbol: \"3\",\n backscattering: [\n [\"A\", \"1E\", \"2E\"],\n [\"A\", \"1E\", \"2E\"],\n [\"A\", \"1E\", \"2E\"],\n ],\n },\n\n C3i: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n 3: [NI],\n 4: [sz(NPI3)],\n 5: [sz(PI3)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1],\n \"1Eg\": [1, W2, W, 1, W2, W],\n \"2Eg\": [1, W, W2, 1, W, W2],\n Au: [1, 1, 1, -1, -1, -1],\n \"1Eu\": [1, W2, W, -1, [-W2[0], -W2[1]], [-W[0], -W[1]]],\n \"2Eu\": [1, W, W2, -1, [-W[0], -W[1]], [-W2[0], -W2[1]]],\n },\n raman: [\"Ag\", \"1Eg\", \"2Eg\"],\n infrared: [\"Au\", \"1Eu\", \"2Eu\"],\n hmSymbol: \"-3\",\n backscattering: [\n [\"Ag\", \"1Eg\", \"2Eg\"],\n [\"Ag\", \"1Eg\", \"2Eg\"],\n [\"Ag\", \"1Eg\", \"2Eg\"],\n ],\n },\n\n D3: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1],\n A2: [1, 1, -1],\n E: [2, -1, 0],\n },\n raman: [\"A1\", \"E\"],\n infrared: [\"A2\", \"E\"],\n hmSymbol: \"32\",\n backscattering: [\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n ],\n },\n\n C3v: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1],\n A2: [1, 1, -1],\n E: [2, -1, 0],\n },\n raman: [\"A1\", \"E\"],\n infrared: [\"A1\", \"E\"],\n hmSymbol: \"3m\",\n backscattering: [\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n ],\n },\n\n D3d: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 3: [NI],\n 4: [sz(NPI3), sz(PI3)],\n 5: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1],\n A2g: [1, 1, -1, 1, 1, -1],\n Eg: [2, -1, 0, 2, -1, 0],\n A1u: [1, 1, 1, -1, -1, -1],\n A2u: [1, 1, -1, -1, -1, 1],\n Eu: [2, -1, 0, -2, 1, 0],\n },\n raman: [\"A1g\", \"Eg\"],\n infrared: [\"A2u\", \"Eu\"],\n hmSymbol: \"-3m\",\n backscattering: [\n [\"A1g\", \"Eg\"],\n [\"A1g\", \"Eg\"],\n [\"A1g\", \"Eg\"],\n ],\n },\n\n // =======================================================================\n // HEXAGONAL\n // =======================================================================\n\n C6: {\n classes: {\n 0: [I],\n 1: [rz(PI3)],\n 2: [rz(TPI3)],\n 3: [rz(PI)],\n 4: [rz(NTPI3)],\n 5: [rz(-PI3)],\n },\n characterTable: {\n A: [1, 1, 1, 1, 1, 1],\n B: [1, -1, 1, -1, 1, -1],\n \"1E2\": [1, W, W2, 1, W, W2],\n \"2E2\": [1, W2, W, 1, W2, W],\n \"1E1\": [1, [-W[0], -W[1]], W2, -1, W, [-W2[0], -W2[1]]],\n \"2E1\": [1, [-W2[0], -W2[1]], W, -1, W2, [-W[0], -W[1]]],\n },\n raman: [\"A\", \"1E2\", \"2E2\", \"1E1\", \"2E1\"],\n infrared: [\"A\", \"1E1\", \"2E1\"],\n hmSymbol: \"6\",\n backscattering: [\n [\"A\", \"1E1\", \"2E1\", \"1E2\", \"2E2\"],\n [\"A\", \"1E1\", \"2E1\", \"1E2\", \"2E2\"],\n [\"A\", \"1E2\", \"2E2\"],\n ],\n },\n\n C3h: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n 3: [sz(0)],\n 4: [sz(NTPI3)],\n 5: [sz(TPI3)],\n },\n characterTable: {\n \"A'\": [1, 1, 1, 1, 1, 1],\n \"A''\": [1, 1, 1, -1, -1, -1],\n \"2E'\": [1, W, W2, 1, W, W2],\n \"1E'\": [1, W2, W, 1, W2, W],\n \"2E''\": [1, W, W2, -1, [-W[0], -W[1]], [-W2[0], -W2[1]]],\n \"1E''\": [1, W2, W, -1, [-W2[0], -W2[1]], [-W[0], -W[1]]],\n },\n raman: [\"A'\", \"1E'\", \"2E'\", \"1E''\", \"2E''\"],\n infrared: [\"A''\", \"1E'\", \"2E'\"],\n hmSymbol: \"-6\",\n backscattering: [\n [\"A'\", \"1E''\", \"2E''\", \"1E'\", \"2E'\"],\n [\"A'\", \"1E''\", \"2E''\", \"1E'\", \"2E'\"],\n [\"A'\", \"1E'\", \"2E'\"],\n ],\n },\n\n C6h: {\n classes: {\n 0: [I],\n 1: [rz(PI3)],\n 2: [rz(TPI3)],\n 3: [rz(PI)],\n 4: [rz(NTPI3)],\n 5: [rz(-PI3)],\n 6: [NI],\n 7: [sz(NTPI3)],\n 8: [sz(-PI3)],\n 9: [sz(0)],\n 10: [sz(PI3)],\n 11: [sz(TPI3)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n Bg: [1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1],\n \"1E2g\": [1, W, W2, 1, W, W2, 1, W, W2, 1, W, W2],\n \"2E2g\": [1, W2, W, 1, W2, W, 1, W2, W, 1, W2, W],\n \"1E1g\": [\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n ],\n \"2E1g\": [\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n ],\n Au: [1, 1, 1, 1, 1, 1, -1, -1, -1, -1, -1, -1],\n Bu: [1, -1, 1, -1, 1, -1, -1, 1, -1, 1, -1, 1],\n \"1E2u\": [\n 1,\n W,\n W2,\n 1,\n W,\n W2,\n -1,\n [-W[0], -W[1]],\n [-W2[0], -W2[1]],\n -1,\n [-W[0], -W[1]],\n [-W2[0], -W2[1]],\n ],\n \"2E2u\": [\n 1,\n W2,\n W,\n 1,\n W2,\n W,\n -1,\n [-W2[0], -W2[1]],\n [-W[0], -W[1]],\n -1,\n [-W2[0], -W2[1]],\n [-W[0], -W[1]],\n ],\n \"1E1u\": [\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n -1,\n W,\n [-W2[0], -W2[1]],\n 1,\n [-W[0], -W[1]],\n W2,\n ],\n \"2E1u\": [\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n -1,\n W2,\n [-W[0], -W[1]],\n 1,\n [-W2[0], -W2[1]],\n W,\n ],\n },\n raman: [\"Ag\", \"1E2g\", \"2E2g\", \"1E1g\", \"2E1g\"],\n infrared: [\"Au\", \"1E1u\", \"2E1u\"],\n hmSymbol: \"6/m\",\n backscattering: [\n [\"Ag\", \"1E1g\", \"2E1g\", \"1E2g\", \"2E2g\"],\n [\"Ag\", \"1E1g\", \"2E1g\", \"1E2g\", \"2E2g\"],\n [\"Ag\", \"1E2g\", \"2E2g\"],\n ],\n },\n\n D6: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI3), rz(-PI3)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [ry(PI), rAxis(AX_SQ3_1_0, PI), rAxis(AX_SQ3_N1_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1, 1],\n A2: [1, 1, 1, 1, -1, -1],\n B1: [1, -1, 1, -1, 1, -1],\n B2: [1, -1, 1, -1, -1, 1],\n E2: [2, 2, -1, -1, 0, 0],\n E1: [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1\", \"E1\", \"E2\"],\n infrared: [\"A2\", \"E1\"],\n hmSymbol: \"622\",\n backscattering: [\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E2\"],\n ],\n },\n\n C6v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI3), rz(-PI3)],\n 4: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n 5: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1, 1],\n A2: [1, 1, 1, 1, -1, -1],\n B1: [1, -1, 1, -1, 1, -1],\n B2: [1, -1, 1, -1, -1, 1],\n E2: [2, 2, -1, -1, 0, 0],\n E1: [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1\", \"E1\", \"E2\"],\n infrared: [\"A1\", \"E1\"],\n hmSymbol: \"6mm\",\n backscattering: [\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E2\"],\n ],\n },\n\n D3h: {\n classes: {\n 0: [I],\n 1: [sz(0)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [sz(TPI3), sz(NTPI3)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n \"A1'\": [1, 1, 1, 1, 1, 1],\n \"A2'\": [1, 1, 1, 1, -1, -1],\n \"A1''\": [1, -1, 1, -1, 1, -1],\n \"A2''\": [1, -1, 1, -1, -1, 1],\n \"E'\": [2, 2, -1, -1, 0, 0],\n \"E''\": [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1'\", \"E'\", \"E''\"],\n infrared: [\"A2''\", \"E'\"],\n hmSymbol: \"-6m2\",\n backscattering: [\n [\"A1'\", \"E'\", \"E''\"],\n [\"A1'\", \"E'\", \"E''\"],\n [\"A1'\", \"E'\"],\n ],\n },\n\n D6h: {\n classes: {\n 0: [I],\n 1: [rz(PI3), rz(-PI3)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [ry(PI), rAxis(AX_SQ3_1_0, PI), rAxis(AX_SQ3_N1_0, PI)],\n 6: [NI],\n 7: [sz(TPI3), sz(NTPI3)],\n 8: [sz(PI3), sz(-PI3)],\n 9: [sz(0)],\n 10: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n 11: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n A2g: [1, 1, 1, 1, -1, -1, 1, 1, 1, 1, -1, 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A matrix backed by a row-major Float64Array. /\nexport interface Matrix {\n readonly rows: number;\n readonly cols: number;\n readonly data: Float64Array;\n}\n\n/* Create a new Matrix with the given dimensions, optionally populated from an iterable.\n * @param rows - Number of rows.\n * @param cols - Number of columns.\n * @param data - Optional iterable of values to fill the matrix.\n * @returns A new Matrix. /\nexport function createMatrix(\n rows: number,\n cols: number,\n data?: Iterable<number>,\n): Matrix {\n const size = rows cols;\n\n const buffer = data ? Float64Array.from(data) : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(`Expected ${size} values, got ${buffer.length}`);\n }\n\n return {\n rows,\n cols,\n data: buffer,\n };\n}\n\n/** Return an identity matrix of the given size.\n * @param size - Number of rows and columns.\n * @returns A square identity matrix. /\nexport function identity(size: number): Matrix {\n const data = new Float64Array(size size);\n\n for (let i = 0; i < size; i++) {\n data[i * size + i] = 1;\n }\n\n return {\n rows: size,\n cols: size,\n data,\n };\n}\n\n/** Return a deep copy of the given matrix.\n * @param matrix - Matrix to clone.\n * @returns A new Matrix with copied data. /\nexport function clone(matrix: Matrix): Matrix {\n return {\n rows: matrix.rows,\n cols: matrix.cols,\n data: new Float64Array(matrix.data),\n };\n}\n\n/* Compute the linear index for the given (row, col) in a row-major layout.\n \n Useful for general matrix element access.\n * Performance-critical inner loops should generally use direct offset arithmetic.\n \n @param cols - Number of columns in the matrix.\n * @param row - Row index.\n * @param col - Column index.\n * @returns Linear index into the data array.\n /\nexport function index(cols: number, row: number, col: number): number {\n return row cols + col;\n}\n","/** Shared floating-point comparison threshold. /\nexport const EPSILON = 1e-12;\n","import { EPSILON } from \"./constants\";\n\n/* Zero-out values within EPSILON of zero. /\nexport function clean(x: number): number {\n return Math.abs(x) < EPSILON ? 0 : x;\n}\n\n/* Greatest common divisor. /\nexport function gcd(a: number, b: number): number {\n a = Math.abs(a);\n b = Math.abs(b);\n while (b !== 0) {\n [a, b] = [b, a % b];\n }\n return a;\n}\n\n/* Least common multiple. /\nexport function lcm(a: number, b: number): number {\n return (Math.abs(a) / gcd(a, b)) Math.abs(b);\n}\n","import { createMatrix, Matrix } from \"../matrix/matrix\";\nimport { clean } from \"../math/numeric\";\n\n/** A lattice defined by a 3x3 basis matrix (row vectors). /\nexport interface Lattice {\n basis: Matrix;\n}\n\n/* Create a Lattice from 3 diagonal lengths, 9 matrix values, or a Matrix. /\nexport function createLattice(\n data: number[] \| Float64Array \| Matrix \| [number, number, number],\n): Lattice {\n const values =\n data instanceof Float64Array\n ? Array.from(data)\n : \"data\" in data\n ? Array.from(data.data)\n : data;\n\n let m: Float64Array;\n\n if (values.length === 3) {\n const [a, b, c] = values;\n\n m = new Float64Array([a, 0, 0, 0, b, 0, 0, 0, c]);\n } else if (values.length === 9) {\n m = new Float64Array(9);\n\n for (let i = 0; i < 9; i++) {\n m[i] = clean(values[i]);\n }\n } else {\n throw new Error(\"Lattice requires 3 or 9 values\");\n }\n\n return {\n basis: createMatrix(3, 3, m),\n };\n}\n","import { Matrix, createMatrix } from \"../matrix\";\n\n/* Multiply two matrices (matrix product).\n * @param a - Left matrix.\n * @param b - Right matrix.\n * @returns A new Matrix containing the product. /\nexport function mul(a: Matrix, b: Matrix): Matrix {\n if (a.cols !== b.rows) {\n throw new Error(\"Invalid matrix multiplication dimensions\");\n }\n\n const out = createMatrix(a.rows, b.cols);\n\n const aRows = a.rows;\n const aCols = a.cols;\n const bCols = b.cols;\n\n const ad = a.data;\n const bd = b.data;\n const od = out.data;\n\n // Iterate row → k → col so B and the output are accessed sequentially\n // in their row-major layout, improving cache locality.\n for (let row = 0; row < aRows; row++) {\n const aOffset = row aCols;\n const outOffset = row * bCols;\n\n for (let k = 0; k < aCols; k++) {\n const aik = ad[aOffset + k];\n const bOffset = k * bCols;\n\n for (let col = 0; col < bCols; col++) {\n od[outOffset + col] += aik * bd[bOffset + col];\n }\n }\n }\n\n return out;\n}\n","import { Matrix, createMatrix } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a 3x3 matrix using cofactors.\n * @param m - A 3x3 matrix.\n * @returns The inverse Matrix. /\nexport function inverse3x3(m: Matrix): Matrix {\n if (m.rows !== 3 \|\| m.cols !== 3) {\n throw new Error(\"Expected 3x3 matrix\");\n }\n\n const a00 = m.data[0],\n a01 = m.data[1],\n a02 = m.data[2];\n const a10 = m.data[3],\n a11 = m.data[4],\n a12 = m.data[5];\n const a20 = m.data[6],\n a21 = m.data[7],\n a22 = m.data[8];\n\n const c00 = a11 a22 - a12 * a21;\n const c01 = a12 * a20 - a10 * a22;\n const c02 = a10 * a21 - a11 * a20;\n\n const c10 = a02 * a21 - a01 * a22;\n const c11 = a00 * a22 - a02 * a20;\n const c12 = a01 * a20 - a00 * a21;\n\n const c20 = a01 * a12 - a02 * a11;\n const c21 = a02 * a10 - a00 * a12;\n const c22 = a00 * a11 - a01 * a10;\n\n const det = a00 * c00 + a01 * c01 + a02 * c02;\n\n if (Math.abs(det) < EPSILON) {\n throw new Error(\"Singular matrix\");\n }\n\n const invDet = 1 / det;\n\n const out = createMatrix(3, 3);\n\n out.data[0] = c00 * invDet;\n out.data[1] = c10 * invDet;\n out.data[2] = c20 * invDet;\n\n out.data[3] = c01 * invDet;\n out.data[4] = c11 * invDet;\n out.data[5] = c21 * invDet;\n\n out.data[6] = c02 * invDet;\n out.data[7] = c12 * invDet;\n out.data[8] = c22 * invDet;\n\n return out;\n}\n","import { Matrix, createMatrix, index } from \"../matrix\";\n\n/** Transpose the given matrix (swap rows and columns).\n * @param matrix - Input matrix.\n * @returns A new transposed Matrix. /\nexport function transpose(matrix: Matrix): Matrix {\n const rows = matrix.rows;\n const cols = matrix.cols;\n\n const data = matrix.data;\n const out = createMatrix(cols, rows);\n const od = out.data;\n\n for (let row = 0; row < rows; row++) {\n const rowOffset = row cols;\n\n for (let col = 0; col < cols; col++) {\n od[col * rows + row] = data[rowOffset + col];\n }\n }\n\n return out;\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Site } from \"@/core/site/site\";\nimport type { Structure } from \"../structure\";\n\n/** Apply a transformation basis matrix to a structure.\n * The new lattice is P * oldBasis and fractional coordinates are P^{-T} * oldFrac,\n * preserving Cartesian positions.\n * @param structure - The input structure.\n * @param basis - A 3x3 transformation matrix.\n * @returns A new Structure with transformed lattice and sites. /\nexport function applyTransformationBasis(\n structure: Structure,\n basis: Matrix,\n): Structure {\n const invP = inverse3x3(basis);\n const newBasis = mul(basis, structure.lattice.basis);\n\n const sites: Site[] = structure.sites.map((site) => {\n const f = site.frac;\n const vec = {\n rows: 3,\n cols: 1,\n data: new Float64Array([f[0], f[1], f[2]]),\n };\n const result = mul(transpose(invP), vec);\n\n return {\n ...site,\n frac: new Float64Array([result.data[0], result.data[1], result.data[2]]),\n };\n });\n\n return {\n lattice: createLattice(newBasis),\n sites,\n };\n}\n","import { Site } from \"../../site/site\";\n\n/* Sort sites by species symbol, then by fractional coordinates (x, y, z). Returns a new array. /\nexport function sortSites(sites: Site[]): Site[] {\n return [...sites].sort((a, b) => {\n const sp = a.species.symbol.localeCompare(b.species.symbol);\n if (sp !== 0) return sp;\n if (a.frac[0] !== b.frac[0]) return a.frac[0] - b.frac[0];\n if (a.frac[1] !== b.frac[1]) return a.frac[1] - b.frac[1];\n return a.frac[2] - b.frac[2];\n });\n}\n","import { Structure } from \"../../structure/structure\";\nimport { sortSites } from \"./sortSites\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nfunction wrap(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < EPSILON ? 0 : v;\n}\n\n/* Return a copy with fractional coordinates wrapped to [0, 1), near-zero values cleaned, and sites sorted by species then coordinates. /\nexport function canonicalize(structure: Structure): Structure {\n const sites = structure.sites.map((site) => ({\n ...site,\n frac: new Float64Array([\n wrap(clean(site.frac[0])),\n wrap(clean(site.frac[1])),\n wrap(clean(site.frac[2])),\n ]),\n }));\n\n return { ...structure, sites: sortSites(sites) };\n}\n","import { Structure } from \"../structure\";\nimport { canonicalize } from \"./canonicalize\";\nimport { Vec3 } from \"../../site/site\";\n\nfunction toFixedArray(v: Vec3, precision = 8): string {\n return Array.from(v)\n .map((x) => x.toFixed(precision))\n .join(\",\");\n}\n\nfunction fnv1a(str: string): number {\n let hash = 2166136261;\n\n for (let i = 0; i < str.length; i++) {\n hash ^= str.charCodeAt(i);\n hash = 16777619;\n }\n\n return hash >>> 0;\n}\n\n/** FNV-1a hash of a canonicalized structure (lattice + sorted sites). /\nexport function hashStructure(structure: Structure): number {\n const s = canonicalize(structure);\n\n const lattice = s.lattice.basis.data;\n const latticeKey = toFixedArray(lattice);\n\n const sitesKey = s.sites\n .map((site) => {\n return site.species.symbol + \":\" + toFixedArray(site.frac);\n })\n .sort()\n .join(\"\|\");\n\n const key = latticeKey + \"::\" + sitesKey;\n\n return fnv1a(key);\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Append a single site to the structure. /\nexport function appendSite(structure: Structure, site: Site): Structure {\n const sites = structure.sites.slice();\n sites.push(site);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Append multiple sites to the structure. /\nexport function appendSites(\n structure: Structure,\n sitesToAppend: readonly Site[],\n): Structure {\n return {\n ...structure,\n sites: [...structure.sites, ...sitesToAppend],\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Insert a single site at the given index. /\nexport function insertSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const oldSites = structure.sites;\n const sites = new Array(oldSites.length + 1);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n sites[index] = site;\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + 1] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Insert multiple sites starting at the given index. /\nexport function insertSites(\n structure: Structure,\n index: number,\n sitesToInsert: readonly Site[],\n): Structure {\n const oldSites = structure.sites;\n const n = sitesToInsert.length;\n\n const sites = new Array(oldSites.length + n);\n\n for (let i = 0; i < index; i++) {\n sites[i] = oldSites[i];\n }\n\n for (let i = 0; i < n; i++) {\n sites[index + i] = sitesToInsert[i];\n }\n\n for (let i = index; i < oldSites.length; i++) {\n sites[i + n] = oldSites[i];\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Structure } from \"../../structure\";\n\n/* Remove the site at the given index. /\nexport function removeSite(structure: Structure, index: number): Structure {\n const sites = structure.sites.slice();\n sites.splice(index, 1);\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Remove sites at the given indices. /\nexport function removeSites(\n structure: Structure,\n indices: readonly number[],\n): Structure {\n const remove = new Set(indices);\n\n return {\n ...structure,\n sites: structure.sites.filter((_, i) => !remove.has(i)),\n };\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n/* Replace a single site at the given index. /\nexport function replaceSite(\n structure: Structure,\n index: number,\n site: Site,\n): Structure {\n const sites = structure.sites.slice();\n sites[index] = site;\n\n return {\n ...structure,\n sites,\n };\n}\n\n/* Replace multiple sites at the given indices. /\nexport function replaceSites(\n structure: Structure,\n replacements: readonly {\n index: number;\n site: Site;\n }[],\n): Structure {\n const sites = structure.sites.slice();\n\n for (const { index, site } of replacements) {\n sites[index] = site;\n }\n\n return {\n ...structure,\n sites,\n };\n}\n","import { Vector } from \"../../vector\";\n\n/* Compute the 3D cross product of two vectors.\n * @param a - First 3D vector.\n * @param b - Second 3D vector.\n * @returns The cross product vector. /\nexport function cross(a: Vector, b: Vector): Vector {\n if (a.length !== 3 \|\| b.length !== 3) {\n throw new Error(\"Cross product requires 3D vectors\");\n }\n\n return new Float64Array([\n a[1] b[2] - a[2] * b[1],\n a[2] * b[0] - a[0] * b[2],\n a[0] * b[1] - a[1] * b[0],\n ]);\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the Euclidean norm (magnitude) of a vector.\n * @param v - Input vector.\n * @returns The Euclidean norm. /\nexport function norm(v: Vector): number {\n let sum = 0;\n\n for (let i = 0; i < v.length; i++) {\n const x = v[i];\n sum += x x;\n }\n\n return Math.sqrt(sum);\n}\n","import { Vector } from \"../../vector\";\nimport { norm } from \"./norm\";\n\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Return a unit vector in the direction of v.\n * @param v - Input vector.\n * @returns A normalized unit vector. /\nexport function normalize(v: Vector): Vector {\n const n = norm(v);\n\n if (n < EPSILON) {\n throw new Error(\"Cannot normalize zero vector\");\n }\n\n const out = new Float64Array(v.length);\n\n for (let i = 0; i < v.length; i++) {\n out[i] = v[i] / n;\n }\n\n return out;\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { cross } from \"@/core/matrix/operations/vector/cross\";\nimport { normalize } from \"@/core/matrix/operations/vector/normalize\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/\n Rotate the lattice so that the given Cartesian direction maps to the new c-axis\n * (third lattice vector). Atom Cartesian positions are preserved exactly.\n \n NOTE: this only guarantees the new c-axis aligns with `normal` when the original\n * third lattice vector is parallel to `normal`. For slab construction, the caller\n * must first apply `calculateScaleFactor` + `supercell` to orient the cell.\n \n @param structure - The input structure.\n * @param normal - A 3D Cartesian direction vector (need not be unit).\n * @returns A new Structure with rotated lattice and sites.\n /\nexport function reorientToNormal(\n structure: Structure,\n normal: Float64Array \| number[],\n): Structure {\n const n = normalize(new Float64Array(normal));\n\n let e1: Float64Array;\n const ref = new Float64Array([1, 0, 0]);\n\n if (Math.abs(Math.abs(n[0]) - 1) < EPSILON) {\n e1 = normalize(cross(n, new Float64Array([0, 1, 0])));\n } else {\n e1 = normalize(cross(n, ref));\n }\n\n const e2 = cross(n, e1);\n\n const R = createMatrix(3, 3, [\n e1[0], e2[0], n[0],\n e1[1], e2[1], n[1],\n e1[2], e2[2], n[2],\n ]);\n\n return applyTransformationBasis(structure, R);\n}\n","import { createMatrix } from \"@/core/matrix/matrix\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport type { Structure } from \"../../structure\";\nimport { EPSILON } from \"@/core/math/constants\";\n\n/\n Add vacuum along the c-axis by stretching the c-vector.\n * Atom Cartesian positions are preserved exactly.\n * @param structure - The input structure (should already be reoriented with surface normal along c).\n * @param thickness - Vacuum thickness in the same length units as the lattice.\n * @returns A new Structure with extended c-vector.\n /\nexport function addVacuum(structure: Structure, thickness: number): Structure {\n if (thickness <= 0) return structure;\n\n const b = structure.lattice.basis.data;\n const cVec = new Float64Array([b[6], b[7], b[8]]);\n const cLength = norm(cVec);\n\n if (cLength < EPSILON) {\n throw new Error(\"c-vector has zero length\");\n }\n\n const scale = (cLength + thickness) / cLength;\n const P = createMatrix(3, 3, [1, 0, 0, 0, 1, 0, 0, 0, scale]);\n\n return applyTransformationBasis(structure, P);\n}\n","import { Matrix, clone } from \"../matrix\";\n\nimport { EPSILON } from \"../../math/constants\";\n\nexport interface LUDecomposition {\n readonly LU: Matrix;\n readonly piv: Int32Array;\n readonly sign: number;\n readonly singular: boolean;\n}\n\n/* Compute the LU decomposition of a square matrix with partial pivoting.\n * @param A - A square matrix.\n * @returns The LU decomposition. /\nexport function lu(A: Matrix): LUDecomposition {\n if (A.rows !== A.cols) {\n throw new Error(\"LU decomposition requires a square matrix\");\n }\n\n const n = A.rows;\n const LU = clone(A);\n const data = LU.data;\n const piv = new Int32Array(n);\n\n for (let i = 0; i < n; i++) {\n piv[i] = i;\n }\n\n let sign = 1;\n\n for (let k = 0; k < n; k++) {\n const rowK = k n;\n\n let pivot = k;\n let max = Math.abs(data[rowK + k]);\n\n // Find pivot row.\n for (let i = k + 1; i < n; i++) {\n const rowI = i * n;\n const v = Math.abs(data[rowI + k]);\n\n if (v > max) {\n max = v;\n pivot = i;\n }\n }\n\n if (max < EPSILON) {\n return {\n LU,\n piv,\n sign,\n singular: true,\n };\n }\n\n // Swap rows.\n if (pivot !== k) {\n const rowP = pivot * n;\n\n for (let j = 0; j < n; j++) {\n const tmp = data[rowK + j];\n data[rowK + j] = data[rowP + j];\n data[rowP + j] = tmp;\n }\n\n const tmp = piv[k];\n piv[k] = piv[pivot];\n piv[pivot] = tmp;\n\n sign = -sign;\n }\n\n const pivotVal = data[rowK + k];\n\n // Eliminate below pivot.\n for (let i = k + 1; i < n; i++) {\n const rowI = i * n;\n const factor = data[rowI + k] / pivotVal;\n\n data[rowI + k] = factor;\n\n for (let j = k + 1; j < n; j++) {\n data[rowI + j] -= factor * data[rowK + j];\n }\n }\n }\n\n return {\n LU,\n piv,\n sign,\n singular: false,\n };\n}\n","import { Matrix } from \"../matrix\";\nimport { lu } from \"./lu\";\n\n/** Compute the determinant of a square matrix using LU decomposition (O(n³)).\n * @param matrix - A square matrix.\n * @returns The determinant value. /\nexport function determinant(matrix: Matrix): number {\n if (matrix.rows !== matrix.cols) {\n throw new Error(\"Determinant requires a square matrix\");\n }\n\n const n = matrix.rows;\n\n // fast path for BZ / geometry\n if (n === 3) {\n const m = matrix.data;\n\n return (\n m[0] (m[4] * m[8] - m[5] * m[7]) -\n m[1] * (m[3] * m[8] - m[5] * m[6]) +\n m[2] * (m[3] * m[7] - m[4] * m[6])\n );\n }\n\n if (n === 1) {\n return matrix.data[0];\n }\n\n if (n === 2) {\n return matrix.data[0] * matrix.data[3] - matrix.data[1] * matrix.data[2];\n }\n\n const { LU, sign, singular } = lu(matrix);\n\n if (singular) return 0;\n\n const data = LU.data;\n let det = sign;\n\n for (let i = 0; i < n; i++) {\n det = data[i n + i];\n }\n\n return det;\n}\n","import { Vector } from \"../../vector\";\n\n/** Compute the dot product of two vectors.\n * @param a - First vector.\n * @param b - Second vector.\n * @returns The dot product. /\nexport function dot(a: Vector, b: Vector): number {\n if (a.length !== b.length) {\n throw new Error(\"Dot product requires same-length vectors\");\n }\n\n let sum = 0;\n\n for (let i = 0; i < a.length; i++) {\n sum += a[i] b[i];\n }\n\n return sum;\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse3x3 } from \"../matrix/operations/inverse/inverse3x3\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/** Compute the inverse of the lattice basis matrix. /\nexport function inverse(lattice: Lattice): Matrix {\n return inverse3x3(lattice.basis);\n}\n","import { Lattice, createLattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\n/* Compute the crystallographic reciprocal lattice (without 2pi scaling). /\nexport function reciprocalLatticeCrystallographic(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n return createLattice(invT.data);\n}\n","import { createMatrix, type Matrix } from \"@/core/matrix/matrix\";\nimport { determinant } from \"@/core/matrix/operations/determinant\";\nimport { dot } from \"@/core/matrix/operations/vector/dot\";\nimport { norm } from \"@/core/matrix/operations/vector/norm\";\nimport { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport type { Lattice } from \"@/core/lattice/lattice\";\nimport { EPSILON } from \"@/core/math/constants\";\nimport { gcd, lcm } from \"@/core/math/numeric\";\n\nfunction reduceVector(v: number[]): number[] {\n let g = 0;\n for (const x of v) {\n g = gcd(g, Math.abs(Math.round(x)));\n }\n if (g <= 1) return v;\n return v.map((x) => Math.round(x / g));\n}\n\n/*\n Calculate the slab scale factor following pymatgen's `calculate_scaling_factor` algorithm.\n \n Given Miller indices (h, k, l), builds a 3×3 integer matrix U such that:\n * - Rows 0 and 1 are real-space vectors perpendicular to the surface normal (in-plane).\n * - Row 2 is a real-space vector with maximal projection onto the surface normal (c-direction).\n \n The key insight: a real-space vector v = r·lattice is perpendicular to the (hkl) surface\n * normal iff r·[h,k,l] = 0. In-plane rows are built as LCM combinations of lattice vectors\n * whose integer coefficients cancel the dot product with the Miller index.\n \n @param millerIndex - The Miller indices [h, k, l].\n * @param lattice - The crystal lattice.\n * @returns A 3×3 integer Matrix (the scale factor).\n /\nexport function calculateScaleFactor(\n millerIndex: [number, number, number],\n lattice: Lattice,\n): Matrix {\n const [h, k, l] = millerIndex;\n\n // Surface normal in Cartesian from reciprocal lattice\n const recip = reciprocalLatticeCrystallographic(lattice);\n const rb = recip.basis.data;\n const normalRaw = new Float64Array([\n h rb[0] + k * rb[3] + l * rb[6],\n h * rb[1] + k * rb[4] + l * rb[7],\n h * rb[2] + k * rb[5] + l * rb[8],\n ]);\n const normalLen = norm(normalRaw);\n if (normalLen < EPSILON) {\n throw new Error(\"Miller index [0,0,0] is invalid\");\n }\n const normal = new Float64Array(normalRaw.map((x) => x / normalLen));\n\n const basis = lattice.basis.data;\n const millerArr = [h, k, l];\n\n // Classify lattice vectors: in-plane (miller[i]==0) vs non-orthogonal\n const slabScaleFactor: number[][] = [];\n const nonOrthInd: [number, number][] = []; // [index, projection onto normal]\n\n for (let idx = 0; idx < 3; idx++) {\n if (millerArr[idx] === 0) {\n // Lattice vector is already in the surface plane\n const row = [0, 0, 0];\n row[idx] = 1;\n slabScaleFactor.push(row);\n } else {\n const aIdx = new Float64Array([\n basis[idx * 3],\n basis[idx * 3 + 1],\n basis[idx * 3 + 2],\n ]);\n const aLen = norm(aIdx);\n const d = Math.abs(dot(normal, aIdx)) / aLen;\n nonOrthInd.push([idx, d]);\n }\n }\n\n // Pick the vector with maximum projection onto normal as the c-direction\n let cIndex = nonOrthInd[0][0];\n let maxProj = nonOrthInd[0][1];\n for (const [idx, proj] of nonOrthInd) {\n if (proj > maxProj) {\n cIndex = idx;\n maxProj = proj;\n }\n }\n\n // Build in-plane vectors from non-orthogonal pairs using LCM combinations\n // For pair (ii, jj): row[ii] = -lcm/m[ii], row[jj] = lcm/m[jj]\n // This ensures row·[h,k,l] = (-lcm/m[ii])m[ii] + (lcm/m[jj])m[jj] = -lcm + lcm = 0\n if (nonOrthInd.length > 1) {\n const millerNonZero = nonOrthInd.map(([idx]) => Math.abs(millerArr[idx]));\n let lcmVal = millerNonZero[0];\n for (let i = 1; i < millerNonZero.length; i++) {\n lcmVal = lcm(lcmVal, millerNonZero[i]);\n }\n\n for (let ii = 0; ii < nonOrthInd.length; ii++) {\n for (let jj = ii + 1; jj < nonOrthInd.length; jj++) {\n const iiIdx = nonOrthInd[ii][0];\n const jjIdx = nonOrthInd[jj][0];\n const row = [0, 0, 0];\n row[iiIdx] = -Math.round(lcmVal / millerArr[iiIdx]);\n row[jjIdx] = Math.round(lcmVal / millerArr[jjIdx]);\n slabScaleFactor.push(reduceVector(row));\n if (slabScaleFactor.length === 2) break;\n }\n if (slabScaleFactor.length === 2) break;\n }\n }\n\n // Add c-direction vector: use the lattice vector at cIndex (identity row)\n const cRow = [0, 0, 0];\n cRow[cIndex] = 1;\n slabScaleFactor.push(cRow);\n\n // Build matrix\n const flat = slabScaleFactor.flat();\n let mat = createMatrix(3, 3, flat);\n\n // Ensure positive determinant (left-handed → negate first row)\n if (determinant(mat) < 0) {\n mat = createMatrix(\n 3,\n 3,\n flat.map((x, i) => (i < 3 ? -x : x)),\n );\n }\n\n return mat;\n}\n","import { mul } from \"../matrix/operations/mul\";\nimport { transpose } from \"../matrix/operations/transpose\";\n\nimport { Site } from \"./site\";\nimport { Lattice } from \"../lattice/lattice\";\nimport { Vector } from \"../matrix/vector\";\n\n/** Convert a site's fractional coordinates to Cartesian.\n * @param lattice - The lattice.\n * @param site - The site.\n * @returns Cartesian coordinate vector. /\nexport function cartesian(lattice: Lattice, site: Site): Vector {\n const [x, y, z] = site.frac;\n\n const frac = {\n rows: 3,\n cols: 1,\n data: new Float64Array([x, y, z]),\n };\n\n const basisT = transpose(lattice.basis);\n const result = mul(basisT, frac);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { inverse } from \"../lattice/inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Vector } from \"../matrix/vector\";\nimport { Lattice } from \"../lattice/lattice\";\n\n/* Convert Cartesian coordinates to fractional.\n * @param lattice - The lattice.\n * @param cart - Cartesian vector.\n * @returns Fractional coordinate vector. /\nexport function fractional(lattice: Lattice, cart: Vector): Vector {\n const vec = {\n rows: 3,\n cols: 1,\n data: cart,\n };\n\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const result = mul(invT, vec);\n\n return new Float64Array([result.data[0], result.data[1], result.data[2]]);\n}\n","import { Matrix, createMatrix } from \"../matrix\";\nimport { inverse3x3 } from \"./inverse/inverse3x3\";\n\n/\n Return fractional coordinates (in the original cell) of all lattice points\n * that lie inside the supercell defined by an integer transformation matrix U.\n \n The new cell has basis B' = U @ B. A lattice point at integer vector n\n * maps to fractional coordinate inv(U) @ n in the original cell. We collect\n * all n such that inv(U) @ n has every component in [0, 1).\n \n The number of returned points equals \|det(U)\|.\n \n @param U - A 3×3 integer transformation matrix.\n * @returns An array of 3-element Float64Arrays, each a fractional coordinate.\n /\nexport function latticePointsInSupercell(U: Matrix): Float64Array[] {\n const invU = inverse3x3(U);\n\n // Determine search range: entries of inv(U) scale the integer vectors,\n // so we need to cover enough range. For typical slab scale factors\n // (entries 0, ±1, ±2), ±4 is ample.\n const maxEntry = Math.max(\n ...Array.from(U.data).map(Math.abs),\n 1,\n );\n const range = maxEntry + 2;\n\n const points: Float64Array[] = [];\n\n for (let i = -range; i <= range; i++) {\n for (let j = -range; j <= range; j++) {\n for (let k = -range; k <= range; k++) {\n // frac = invU @ [i, j, k]\n const d = invU.data;\n const f0 = d[0] i + d[1] * j + d[2] * k;\n const f1 = d[3] * i + d[4] * j + d[5] * k;\n const f2 = d[6] * i + d[7] * j + d[8] * k;\n\n if (\n f0 >= -1e-10 && f0 < 1 - 1e-10 &&\n f1 >= -1e-10 && f1 < 1 - 1e-10 &&\n f2 >= -1e-10 && f2 < 1 - 1e-10\n ) {\n points.push(\n new Float64Array([\n Math.max(0, f0),\n Math.max(0, f1),\n Math.max(0, f2),\n ]),\n );\n }\n }\n }\n }\n\n return points;\n}\n","import { createLattice } from \"@/core/lattice/lattice\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { cartesian } from \"@/core/site/cartesian\";\nimport { fractional } from \"@/core/site/fractional\";\nimport { latticePointsInSupercell } from \"@/core/matrix/operations/latticePointsInSupercell\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\nimport type { Structure } from \"../structure\";\nimport type { Site } from \"@/core/site/site\";\n\ntype SupercellSize = number \| [number, number, number] \| Matrix;\n\nfunction isMatrix(size: SupercellSize): size is Matrix {\n return typeof size !== \"number\" && !Array.isArray(size);\n}\n\n/** Create a supercell by applying an integer transformation matrix U.\n \n If `size` is a number or [nx, ny, nz], a diagonal supercell is formed by\n * replicating the structure in each lattice direction.\n \n If `size` is a 3x3 integer Matrix, the general supercell algorithm from\n * pymatgen's `Structure.__mul__` (make_supercell) is used: the new basis\n * is U @ oldBasis and lattice points are replicated by \|det(U)\|.\n \n @param structure - The input structure.\n * @param size - Supercell size: number (isotropic), [nx, ny, nz], or 3x3 integer matrix.\n * @returns A new Structure with the supercell applied.\n /\nexport function supercell(structure: Structure, size: SupercellSize): Structure {\n let U: Matrix;\n\n if (isMatrix(size)) {\n U = size;\n } else {\n const [nx, ny, nz] = typeof size === \"number\" ? [size, size, size] : size;\n U = createMatrix(3, 3, [nx, 0, 0, 0, ny, 0, 0, 0, nz]);\n }\n\n const newBasis = mul(U, structure.lattice.basis);\n const newLattice = createLattice(newBasis);\n\n const fracPoints = latticePointsInSupercell(U);\n\n const sites: Site[] = [];\n\n for (const site of structure.sites) {\n const siteCart = cartesian(structure.lattice, site);\n\n for (const lp of fracPoints) {\n // Lattice point in Cartesian (using new lattice)\n const lpCart = cartesian(newLattice, {\n species: site.species,\n frac: lp,\n });\n\n const pos = new Float64Array([\n siteCart[0] + lpCart[0],\n siteCart[1] + lpCart[1],\n siteCart[2] + lpCart[2],\n ]);\n\n const frac = fractional(newLattice, pos);\n\n // Wrap to [0, 1)\n for (let d = 0; d < 3; d++) {\n frac[d] = frac[d] - Math.floor(frac[d]);\n if (frac[d] > 1 - 1e-10) frac[d] = 0;\n if (frac[d] < 1e-10) frac[d] = 0;\n }\n\n sites.push({\n species: site.species,\n frac,\n });\n }\n }\n\n return {\n lattice: newLattice,\n sites,\n };\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { calculateScaleFactor } from \"./calculateScaleFactor\";\nimport { supercell } from \"../supercell\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /* Number of unit cell replications along c (surface normal). Default 1. /\n layers?: number;\n /* Vacuum thickness in Angstroms. Default 0. /\n vacuum?: number;\n}\n\n/\n Generate a slab oriented along the (hkl) plane, following pymatgen's algorithm.\n \n Steps:\n * 1. Calculate an integer scale factor U that puts in-plane vectors perpendicular\n * to the surface normal, and a c-vector with max projection onto the normal.\n * 2. Apply make_supercell(U) to create an oriented unit cell (OUC).\n * 3. Replicate the OUC along c to get the desired number of layers.\n * 4. Add vacuum by stretching the c-vector.\n \n @param structure - The bulk input structure.\n * @param h - Miller index h.\n * @param k - Miller index k.\n * @param l - Miller index l.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n /\nexport function slabFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n // Step 1: Calculate the scale factor\n const U = calculateScaleFactor([h, k, l], structure.lattice);\n\n // Step 2: Create the oriented unit cell\n const ouc = supercell(structure, U);\n\n // Step 3: Replicate along c\n const replicated = supercell(ouc, [1, 1, layers]);\n\n // Step 4: Add vacuum\n return addVacuum(replicated, vacuum);\n}\n","/* A 3-component vector. /\nexport type Vec3 = Float64Array;\n\n// TODO: these are sort of generic geomtery utils\n// perhaps they would be better served higher up.\n\n/* Wrap a fractional displacement into the minimum-image convention (components in [-0.5, 0.5]). /\nexport function minimumImage(df: Vec3): Float64Array {\n return new Float64Array([\n df[0] - Math.round(df[0]),\n df[1] - Math.round(df[1]),\n df[2] - Math.round(df[2]),\n ]);\n}\n/* Squared distance from a minimum-image vector using the metric tensor G. /\nexport function distanceSquared(mic: Vec3, G: Float64Array): number {\n const x = mic[0],\n y = mic[1],\n z = mic[2];\n\n return (\n x (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z)\n );\n}\n","import { Structure } from \"../../structure\";\nimport { minimumImage } from \"./utils\";\n/** A 3-component vector. /\nexport type Vec3 = Float64Array;\n\n/* Minimum-image displacement vector from site idx1 to site idx2. /\nexport function getDisplacement(\n structure: Structure,\n idx1: number,\n idx2: number,\n): Vec3 {\n const s1 = structure.sites[idx1];\n const s2 = structure.sites[idx2];\n\n return minimumImage([\n s2.frac[0] - s1.frac[0],\n s2.frac[1] - s1.frac[1],\n s2.frac[2] - s1.frac[2],\n ]);\n}\n","import { Lattice } from \"./lattice\";\nimport { inverse } from \"./inverse\";\nimport { transpose } from \"../matrix/operations/transpose\";\nimport { createMatrix } from \"../matrix/matrix\";\nimport { createLattice } from \"./lattice\";\n\nconst TWO_PI = 2 Math.PI;\n\n/** Compute the reciprocal lattice scaled by 2pi. /\nexport function reciprocalLattice(lattice: Lattice): Lattice {\n const inv = inverse(lattice);\n const invT = transpose(inv);\n\n const data = invT.data.map((v) => v * TWO_PI);\n\n return createLattice(data);\n}\n","import { Structure } from \"../../structure\";\nimport { getDisplacement } from \"../distance/getDisplacement\";\nimport { cross } from \"../../../matrix/operations/vector/cross\";\nimport { norm } from \"../../../matrix/operations/vector/norm\";\nimport { cartesian } from \"../../../site/cartesian\";\n\nimport { reciprocalLattice } from \"../../../lattice/reciprocalLattice\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** A plane defined by a unit normal and a point on the plane (Cartesian). /\nexport interface Plane {\n readonly normal: Float64Array;\n readonly point: Float64Array;\n}\n\n/* Plane equation in the form ax + by + cz + d = 0. /\nexport interface PlaneEquation {\n readonly a: number;\n readonly b: number;\n readonly c: number;\n readonly d: number;\n}\n\n/* Plane through three non-collinear sites. /\nexport function planeFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n): Plane {\n // Cartesian displacement vectors\n const r1 = getDisplacement(structure, i, j);\n const r2 = getDisplacement(structure, i, k);\n\n const n = cross(r1, r2);\n const nNorm = norm(n);\n\n if (nNorm < EPSILON) {\n throw new Error(\"Cannot construct plane from collinear sites\");\n }\n\n const normal = new Float64Array([n[0] / nNorm, n[1] / nNorm, n[2] / nNorm]);\n\n // pick a real point on plane (site i), convert properly\n const point = cartesian(structure.lattice, structure.sites[i]);\n\n return { normal, point };\n}\n\n/* Convert a Plane to PlaneEquation coefficients (ax + by + cz + d = 0). /\nexport function planeEquation(plane: Plane): PlaneEquation {\n const { normal, point } = plane;\n\n const d = -(\n normal[0] point[0] +\n normal[1] * point[1] +\n normal[2] * point[2]\n );\n\n return {\n a: normal[0],\n b: normal[1],\n c: normal[2],\n d,\n };\n}\n\n/** Signed distance from a Cartesian point to a plane. /\nexport function distanceFromPlane(\n point: Float64Array,\n plane: PlaneEquation,\n): number {\n const { a, b, c, d } = plane;\n\n const denominator = Math.sqrt(a a + b * b + c * c);\n\n if (denominator < EPSILON) {\n throw new Error(\"Invalid plane normal\");\n }\n\n return (a * point[0] + b * point[1] + c * point[2] + d) / denominator;\n}\n\n/** Signed distance from a site to a plane. /\nexport function distanceFromSiteToPlane(\n structure: Structure,\n siteIndex: number,\n plane: PlaneEquation,\n): number {\n const point = cartesian(structure.lattice, structure.sites[siteIndex]);\n\n return distanceFromPlane(point, plane);\n}\n\n/* Plane from Miller indices (hkl) using the reciprocal lattice. /\nexport function planeFromMillerIndex(\n structure: Structure,\n h: number,\n k: number,\n l: number,\n): Plane {\n const reciprocal = reciprocalLattice(structure.lattice);\n\n const normal = new Float64Array([\n h reciprocal.basis.data[0] +\n k * reciprocal.basis.data[3] +\n l * reciprocal.basis.data[6],\n\n h * reciprocal.basis.data[1] +\n k * reciprocal.basis.data[4] +\n l * reciprocal.basis.data[7],\n\n h * reciprocal.basis.data[2] +\n k * reciprocal.basis.data[5] +\n l * reciprocal.basis.data[8],\n ]);\n\n const length = norm(normal);\n\n if (length < EPSILON) {\n throw new Error(\"Invalid Miller index\");\n }\n\n return {\n normal: new Float64Array([\n normal[0] / length,\n normal[1] / length,\n normal[2] / length,\n ]),\n point: new Float64Array([0, 0, 0]),\n };\n}\n","import { planeFromSites } from \"../geometry/plane\";\nimport { canonicalize } from \"../canonicalize\";\nimport { supercell } from \"../supercell\";\nimport { reorientToNormal } from \"./reorientToNormal\";\nimport { addVacuum } from \"./addVacuum\";\nimport type { Structure } from \"../../structure\";\n\ninterface SlabOptions {\n /** Number of unit cell replications along c (surface normal). Default 1. /\n layers?: number;\n /* Vacuum thickness in lattice length units. Default 0. /\n vacuum?: number;\n}\n\n/\n Generate a slab oriented so the plane through three sites is the surface.\n \n Steps: plane normal → rotation → replicate → add vacuum.\n * Atom Cartesian positions within the slab are preserved exactly.\n \n @param structure - The bulk input structure.\n * @param i - Index of first site defining the surface plane.\n * @param j - Index of second site defining the surface plane.\n * @param k - Index of third site defining the surface plane.\n * @param opts - Slab options.\n * @returns A new Structure representing the slab.\n /\nexport function slabFromSites(\n structure: Structure,\n i: number,\n j: number,\n k: number,\n opts: SlabOptions = {},\n): Structure {\n const { layers = 1, vacuum = 0 } = opts;\n\n const plane = planeFromSites(structure, i, j, k);\n const reoriented = canonicalize(reorientToNormal(structure, plane.normal));\n const replicated = supercell(reoriented, [1, 1, layers]);\n\n return addVacuum(replicated, vacuum);\n}\n","import { dot } from \"../matrix/operations/vector/dot\";\nimport { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n\nimport { Vector } from \"../matrix/vector\";\n\nfunction angle(u: Vector, v: Vector) {\n const denom = norm(u) norm(v);\n if (Math.abs(denom) < 1e-300) throw new Error(\"Zero-length lattice vector\");\n\n const c = dot(u, v) / denom;\n const clamped = Math.max(-1, Math.min(1, c));\n\n return Math.acos(clamped);\n}\n\n/** Compute the three inter-vector angles (alpha, beta, gamma) in radians. /\nexport function angles(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Vector = new Float64Array([m[0], m[1], m[2]]);\n const b: Vector = new Float64Array([m[3], m[4], m[5]]);\n const c: Vector = new Float64Array([m[6], m[7], m[8]]);\n\n const alpha = angle(b, c);\n const beta = angle(a, c);\n const gamma = angle(a, b);\n\n return [alpha, beta, gamma];\n}\n","import { norm } from \"../matrix/operations/vector/norm\";\nimport { Lattice } from \"./lattice\";\n/* Compute the three lattice vector lengths (a, b, c). /\nexport function lengths(lattice: Lattice): [number, number, number] {\n const m = lattice.basis.data;\n\n const a: Float64Array = new Float64Array([m[0], m[1], m[2]]);\n const b: Float64Array = new Float64Array([m[3], m[4], m[5]]);\n const c: Float64Array = new Float64Array([m[6], m[7], m[8]]);\n\n return [norm(a), norm(b), norm(c)];\n}\n","import { transpose } from \"../matrix/operations/transpose\";\nimport { mul } from \"../matrix/operations/mul\";\nimport { Lattice } from \"./lattice\";\nimport { Matrix } from \"../matrix/matrix\";\n\n/* Compute the metric tensor G = A A^T for the lattice basis (row vectors). /\nexport function metricTensor(lattice: Lattice): Matrix {\n const A = lattice.basis;\n\n const AT = transpose(A);\n return mul(A, AT);\n}\n","import { lengths } from \"./lengths\";\nimport { angles } from \"./angles\";\nimport { Lattice } from \"./lattice\";\n\nconst RAD2DEG = 180 / Math.PI;\n\n/* Return lattice parameters (a, b, c, alpha, beta, gamma) with angles in degrees. /\nexport function parameters(\n lattice: Lattice,\n): [number, number, number, number, number, number] {\n const [a, b, c] = lengths(lattice);\n const [alpha, beta, gamma] = angles(lattice);\n\n return [a, b, c, alpha RAD2DEG, beta * RAD2DEG, gamma * RAD2DEG];\n}\n","import { Lattice } from \"./lattice\";\nimport { reciprocalLatticeCrystallographic } from \"./reciprocalLatticeCrystallographic\";\nimport { lengths } from \"./lengths\";\n\n/** Compute k-point grid [Nx, Ny, Nz] from desired spacing in Å⁻¹. /\nexport function kspacingToGrid(\n lattice: Lattice,\n spacing: number,\n): [number, number, number] {\n if (spacing <= 0) {\n throw new Error(\"k-spacing must be positive\");\n }\n\n const rec = reciprocalLatticeCrystallographic(lattice);\n const [b1, b2, b3] = lengths(rec);\n\n return [\n Math.max(1, Math.ceil((b1 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b2 * 2 * Math.PI) / spacing)),\n Math.max(1, Math.ceil((b3 * 2 * Math.PI) / spacing)),\n ];\n}\n","import { createLattice } from \"../lattice\";\nimport { EPSILON } from \"../../math/constants\";\nimport { clean } from \"../../math/numeric\";\n\nconst DEG2RAD = Math.PI / 180;\n\n/** Create a Lattice from conventional cell parameters (angles in degrees). /\nexport function fromParameters(\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n) {\n const alphaR = alpha DEG2RAD;\n const betaR = beta * DEG2RAD;\n const gammaR = gamma * DEG2RAD;\n\n const cosA = Math.cos(alphaR);\n const cosB = Math.cos(betaR);\n const cosG = Math.cos(gammaR);\n const sinG = Math.sin(gammaR);\n\n // lattice vectors\n const v1 = [a, 0, 0];\n\n const v2 = [b * cosG, b * sinG, 0];\n\n // guard against degenerate gamma\n if (Math.abs(sinG) < EPSILON) {\n throw new Error(\"Invalid lattice: gamma too close to 0 or 180 degrees\");\n }\n\n const cx = c * cosB;\n\n const cy = (c * (cosA - cosB * cosG)) / sinG;\n\n const czSquared = c * c - cx * cx - cy * cy;\n\n const cz = Math.sqrt(Math.max(0, czSquared));\n\n return createLattice([\n clean(v1[0]),\n clean(v1[1]),\n clean(v1[2]),\n clean(v2[0]),\n clean(v2[1]),\n clean(v2[2]),\n clean(cx),\n clean(cy),\n clean(cz),\n ]);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/** Create a cubic lattice with side length a. /\nexport function cubic(a: number) {\n return fromParameters(a, a, a, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a hexagonal lattice with side a and height c. /\nexport function hexagonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 120);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a monoclinic lattice (alpha=gamma=90, beta given in degrees). /\nexport function monoclinic(a: number, b: number, c: number, beta: number) {\n return fromParameters(a, b, c, 90, beta, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create an orthorhombic lattice with sides a, b, c and all angles 90. /\nexport function orthorhombic(a: number, b: number, c: number) {\n return fromParameters(a, b, c, 90, 90, 90);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a rhombohedral lattice with side a and equal angles alpha (degrees). /\nexport function rhombohedral(a: number, alpha: number) {\n return fromParameters(a, a, a, alpha, alpha, alpha);\n}\n","import { fromParameters } from \"./fromParameters\";\n\n/* Create a tetragonal lattice with a=b, c, and all angles 90. /\nexport function tetragonal(a: number, c: number) {\n return fromParameters(a, a, c, 90, 90, 90);\n}\n","/\n First-class symmetry engine backed by `@spglib/moyo-wasm`.\n \n This is the primary way to run structure-symmetry analysis in the library.\n * All `analyze_cell`/space-group work goes through the moyo WASM module here.\n * (The lattice Niggli reduction that seekpath used to obtain from the legacy\n * `spglib-wasm/` hand-rolled build is now a pure-TS implementation in\n * `matrix/operations/reduction/niggli.ts`.)\n \n `analyze_cell` is synchronous once the WASM is loaded; the async wrappers\n * below exist to await the one-time `init()` and keep the public API uniform.\n /\n\nimport init, { analyze_cell } from \"@spglib/moyo-wasm\";\nimport type { MoyoDataset } from \"@spglib/moyo-wasm\";\n\nimport { createLattice } from \"@/core/lattice\";\nimport { Structure } from \"../../structure\";\n\nlet ready: Promise<unknown> \| null = null;\n\n/* Ensure the Moyo WASM module is loaded (idempotent). /\nexport function initMoyo() {\n if (!ready) {\n ready = (async () => {\n try {\n // In Node.js (tests) read the wasm bytes from disk; the browser fetches\n // the URL that the package resolves for itself.\n if (typeof process !== \"undefined\" && process.versions?.node) {\n const { readFileSync } = await import(\"fs\");\n const { createRequire } = await import(\"module\");\n const require = createRequire(import.meta.url);\n const wasmPath = require.resolve(\n \"@spglib/moyo-wasm/moyo_wasm_bg.wasm\",\n );\n return await init({ module_or_path: readFileSync(wasmPath) });\n }\n return await init();\n } catch (e) {\n // Don't cache rejections: allow a later call to retry the load.\n ready = null;\n throw e;\n }\n })();\n }\n return ready;\n}\n\n/* Serialize a structure into the Moyo/SPGLIB input representation. /\nfunction toMoyoInput(structure: Structure): {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n} {\n const symbolToId = new Map<string, number>();\n const numbers: number[] = [];\n const positions: number[][] = [];\n\n let counter = 0;\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n counter++;\n }\n\n positions.push(Array.from(site.frac));\n numbers.push(symbolToId.get(symbol)!);\n }\n\n return {\n lattice: { basis: Array.from(structure.lattice.basis.data) },\n positions,\n numbers,\n };\n}\n\n/* Run the symmetry engine on a structure and return the raw Moyo dataset. /\nexport async function analyzeStructure(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Spglib\",\n): Promise<MoyoDataset> {\n await initMoyo();\n return analyze_cell(\n JSON.stringify(toMoyoInput(structure)),\n tolerance,\n setting,\n );\n}\n\n/* Compute primitive and conventional structures plus calculation results via Moyo/SPGLIB. /\nexport async function getSymmetry(\n structure: Structure,\n tolerance = 1e-4,\n setting = \"Spglib\",\n): Promise<{\n primitive: Structure;\n conventional: Structure;\n calculationResults: MoyoDataset;\n}> {\n await initMoyo();\n\n // -----------------------------\n // 1. Run symmetry engine\n // -----------------------------\n const results = await analyzeStructure(structure, tolerance, setting);\n\n // -----------------------------\n // 2. Build reversible mapping\n // -----------------------------\n const symbolToId = new Map<string, number>();\n const idToSymbol = new Map<number, string>();\n\n {\n let counter = 0;\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n if (!symbolToId.has(symbol)) {\n symbolToId.set(symbol, counter);\n idToSymbol.set(counter, symbol);\n counter++;\n }\n }\n }\n\n function build(cell: {\n lattice: { basis: number[] };\n positions: number[][];\n numbers: number[];\n }): Structure {\n const { lattice, positions, numbers } = cell;\n\n const species = [...new Set(numbers)].map((n: number) => ({\n symbol: idToSymbol.get(n)!,\n }));\n\n const sites = positions.map((pos: number[], i: number) => ({\n species: {\n symbol: idToSymbol.get(numbers[i])!,\n },\n frac: new Float64Array(pos),\n }));\n\n return {\n lattice: createLattice(lattice.basis),\n species,\n sites,\n };\n }\n\n // -----------------------------\n // 3. Return both structures\n // -----------------------------\n return {\n primitive: build(results.prim_std_cell),\n conventional: build(results.std_cell),\n calculationResults: results,\n };\n}\n","import { Matrix, createMatrix } from \"../matrix\";\n\n/* Multiply every element of matrix m by scalar k.\n * @param m - Input matrix.\n * @param k - Scalar multiplier.\n * @returns A new scaled Matrix. /\nexport function scale(m: Matrix, k: number): Matrix {\n const out = createMatrix(m.rows, m.cols);\n\n const size = m.data.length;\n\n for (let i = 0; i < size; i++) {\n out.data[i] = m.data[i] k;\n }\n\n return out;\n}\n","import { Matrix, createMatrix, clone, index } from \"../../matrix\";\nimport { EPSILON } from \"../../../math/constants\";\n\n/** Compute the inverse of a square matrix using Gauss-Jordan elimination with partial pivoting.\n * @param m - A square matrix.\n * @returns The inverse Matrix. /\nexport function gjInverse(m: Matrix): Matrix {\n if (m.rows !== m.cols) {\n throw new Error(\"Inverse requires square matrix\");\n }\n\n const n = m.rows;\n const A = clone(m);\n const I = createMatrix(n, n);\n const Adata = A.data;\n const Idata = I.data;\n\n // Initialize identity\n for (let i = 0; i < n; i++) {\n Idata[i n + i] = 1;\n }\n\n for (let i = 0; i < n; i++) {\n let pivotIdx = i * n + i;\n\n // Pivoting\n if (Math.abs(Adata[pivotIdx]) < EPSILON) {\n let swapRow = -1;\n for (let r = i + 1; r < n; r++) {\n if (Math.abs(Adata[r * n + i]) > EPSILON) {\n swapRow = r;\n break;\n }\n }\n if (swapRow === -1) {\n throw new Error(\"Singular matrix\");\n }\n\n // performant inline swap\n const r1Offset = i * n;\n const r2Offset = swapRow * n;\n for (let c = 0; c < n; c++) {\n let tmp = Adata[r1Offset + c];\n Adata[r1Offset + c] = Adata[r2Offset + c];\n Adata[r2Offset + c] = tmp;\n\n tmp = Idata[r1Offset + c];\n Idata[r1Offset + c] = Idata[r2Offset + c];\n Idata[r2Offset + c] = tmp;\n }\n\n pivotIdx = i * n + i;\n }\n\n const pivot = Adata[pivotIdx];\n const invPivot = 1 / pivot;\n\n // Normalize pivot row\n const pivotOffset = i * n;\n for (let c = 0; c < n; c++) {\n Adata[pivotOffset + c] = invPivot;\n Idata[pivotOffset + c] = invPivot;\n }\n\n // Eliminate other rows\n for (let r = 0; r < n; r++) {\n if (r === i) continue;\n\n const factor = Adata[r * n + i];\n if (Math.abs(factor) < EPSILON) continue;\n\n const rOffset = r * n;\n for (let c = 0; c < n; c++) {\n Adata[rOffset + c] -= Adata[pivotOffset + c] * factor;\n Idata[rOffset + c] -= Idata[pivotOffset + c] * factor;\n }\n }\n }\n\n return I;\n}\n","import { reciprocalLatticeCrystallographic } from \"@/core/lattice/reciprocalLatticeCrystallographic\";\nimport { Structure } from \"@/core/structure/structure\";\nimport { dot, mul } from \"@/core/matrix/operations\";\n\nimport { determinant } from \"@/core/matrix/operations\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport { inverse3x3 } from \"@/core/matrix/operations/inverse/inverse3x3\";\nimport { Vector } from \"@/core/matrix/vector\";\n\ninterface Plane {\n normal: Float64Array;\n offset: number;\n}\n\nfunction intersectPlanes(\n p1: Plane,\n p2: Plane,\n p3: Plane,\n tolerance = 1e-10,\n): Float64Array \| null {\n const A = createMatrix(3, 3, [...p1.normal, ...p2.normal, ...p3.normal]);\n\n const detA = determinant(A);\n\n if (Math.abs(detA) < tolerance) return null;\n\n const invA = inverse3x3(A);\n\n const d = createMatrix(3, 1, [p1.offset, p2.offset, p3.offset]);\n\n const res = mul(invA, d).data;\n\n return new Float64Array([res[0], res[1], res[2]]);\n}\n\nfunction key(v: Float64Array) {\n const nx = v[0],\n ny = v[1],\n nz = v[2];\n const inv = 1 / Math.sqrt(nx * nx + ny * ny + nz * nz);\n\n // normalize direction so ±G collapse\n const x = Math.round(nx * inv * 1e6);\n const y = Math.round(ny * inv * 1e6);\n const z = Math.round(nz * inv * 1e6);\n\n return `${x},${y},${z}`;\n}\n\nfunction vkey(v: Float64Array, eps = 1e-6) {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\nfunction isInside(v: Float64Array, planes: Plane[]) {\n const tolerance = 0.0;\n for (const p of planes) {\n const d = p.normal[0] * v[0] + p.normal[1] * v[1] + p.normal[2] * v[2];\n\n if (d > p.offset + tolerance) return false;\n }\n return true;\n}\n\n/** Generate Brillouin zone vertices from the reciprocal crystallographic lattice. /\nexport async function generateBZVertices(\n structure: Structure,\n tolerance: number = 1e-4,\n): Promise<Float64Array[]> {\n const reciprocalLattice = reciprocalLatticeCrystallographic(\n structure.lattice,\n );\n\n const rcLD = reciprocalLattice.basis.data;\n\n const aStar = [rcLD[0], rcLD[1], rcLD[2]];\n const bStar = [rcLD[3], rcLD[4], rcLD[5]];\n const cStar = [rcLD[6], rcLD[7], rcLD[8]];\n\n const range = 2;\n const points: Vector[] = [];\n\n for (let h = -range; h <= range; h++) {\n for (let k = -range; k <= range; k++) {\n for (let l = -range; l <= range; l++) {\n const point = new Float64Array(3);\n\n point[0] = h aStar[0] + k * bStar[0] + l * cStar[0];\n\n point[1] = h * aStar[1] + k * bStar[1] + l * cStar[1];\n\n point[2] = h * aStar[2] + k * bStar[2] + l * cStar[2];\n\n points.push(point);\n }\n }\n }\n\n // remove center point\n const neighbors = points.filter(\n (p) =>\n Math.abs(p[0]) > tolerance \|\|\n Math.abs(p[1]) > tolerance \|\|\n Math.abs(p[2]) > tolerance,\n );\n\n // sort by distance from origin\n neighbors.sort((a, b) => {\n const da = a[0] * a[0] + a[1] * a[1] + a[2] * a[2];\n\n const db = b[0] * b[0] + b[1] * b[1] + b[2] * b[2];\n\n return da - db;\n });\n\n const map = new Map<string, Float64Array>();\n\n for (const p of neighbors) {\n const k = key(p);\n if (!map.has(k)) map.set(k, p);\n }\n\n const uniqueNeighbors = [...map.values()];\n\n // console.log(uniqueNeighbors); // all neighbor recip points\n\n const planes = uniqueNeighbors.slice(0, 26).map((G) => ({\n normal: G,\n offset: dot(G, G) / 2,\n }));\n\n const candidateBZCorners: Float64Array[] = [];\n\n for (let i = 0; i < planes.length; i++) {\n for (let j = i + 1; j < planes.length; j++) {\n for (let k = j + 1; k < planes.length; k++) {\n const v = intersectPlanes(planes[i], planes[j], planes[k], tolerance);\n\n if (!v) continue;\n\n if (isInside(v, planes)) {\n candidateBZCorners.push(v);\n }\n }\n }\n }\n\n const vertexMap = new Map<string, Float64Array>();\n\n for (const v of candidateBZCorners) {\n const k = vkey(v);\n if (!vertexMap.has(k)) {\n vertexMap.set(k, v);\n }\n }\n\n const hullVertices = [...vertexMap.values()];\n\n return hullVertices;\n}\n","/*\n Compute the triangulated polyhedron of the first Brillouin zone from the\n * reciprocal lattice vectors, mirroring `seekpath.brillouinzone.BZ`.\n \n The output matches the `faces_data` consumed by the\n * `brillouinzone-visualizer` web widget:\n * - `triangles_vertices`: all polyhedron vertices\n * - `triangles`: index triples (fan-triangulated convex faces)\n * - `faces`: the flat faces as lists of vertex coordinates\n /\n\nimport { Vector } from \"@/core/matrix/vector\";\nimport { dot, cross, norm } from \"@/core/matrix/operations/vector\";\n\n/* Round a vector direction to a stable key so ±parallel G-vectors collide. /\nfunction directionKey(v: Vector): string {\n const n = norm(v);\n const x = Math.round((v[0] / n) 1e6);\n const y = Math.round((v[1] / n) * 1e6);\n const z = Math.round((v[2] / n) * 1e6);\n return `${x},${y},${z}`;\n}\n\nfunction vertexKey(v: Vector, eps = 1e-6): string {\n return `${Math.round(v[0] / eps)},${Math.round(v[1] / eps)},${Math.round(v[2] / eps)}`;\n}\n\n/*\n Solve the 3x3 system A x = d via Cramer's rule. Returns null if singular.\n * Kept local: the lib `solve` throws on singular matrices, but the corner\n * search needs a null result for near-degenerate plane intersections.\n /\nfunction solve3(A: Vector[], d: number[], tolerance: number): Vector \| null {\n const det = A[0][0] (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n if (Math.abs(det) < tolerance) return null;\n\n const detX = d[0] * (A[1][1] * A[2][2] - A[1][2] * A[2][1]) -\n A[0][1] * (d[1] * A[2][2] - A[1][2] * d[2]) +\n A[0][2] * (d[1] * A[2][1] - A[1][1] * d[2]);\n const detY = A[0][0] * (d[1] * A[2][2] - A[1][2] * d[2]) -\n d[0] * (A[1][0] * A[2][2] - A[1][2] * A[2][0]) +\n A[0][2] * (A[1][0] * d[2] - d[1] * A[2][0]);\n const detZ = A[0][0] * (A[1][1] * d[2] - d[1] * A[2][1]) -\n A[0][1] * (A[1][0] * d[2] - d[1] * A[2][0]) +\n d[0] * (A[1][0] * A[2][1] - A[1][1] * A[2][0]);\n\n return new Float64Array([detX / det, detY / det, detZ / det]);\n}\n\nexport interface BZPolyhedron {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n}\n\n/*\n Compute the first Brillouin zone polyhedron from the reciprocal lattice\n * vectors b1, b2, b3 (rows of the reciprocal lattice matrix).\n /\nexport function getBZPolyhedron(\n b1: number[],\n b2: number[],\n b3: number[],\n supercellSize = 3,\n): BZPolyhedron {\n const r1 = new Float64Array(b1);\n const r2 = new Float64Array(b2);\n const r3 = new Float64Array(b3);\n\n // Reciprocal lattice points, keeping the shortest G-vector per direction\n const best: Map<string, { g: Vector; length2: number }> = new Map();\n for (let i = -supercellSize; i <= supercellSize; i++) {\n for (let j = -supercellSize; j <= supercellSize; j++) {\n for (let k = -supercellSize; k <= supercellSize; k++) {\n if (i === 0 && j === 0 && k === 0) continue;\n const g = new Float64Array([\n i r1[0] + j * r2[0] + k * r3[0],\n i * r1[1] + j * r2[1] + k * r3[1],\n i * r1[2] + j * r2[2] + k * r3[2],\n ]);\n const key = directionKey(g);\n const length2 = dot(g, g);\n const existing = best.get(key);\n if (!existing \|\| length2 < existing.length2) {\n best.set(key, { g, length2 });\n }\n }\n }\n }\n\n // Planes: perpendicular bisectors of the G-vectors (normals g, offset \|g\|^2/2).\n // The faces of the BZ are always among the nearest reciprocal lattice\n // directions, so restricting to the shortest ones is safe and fast.\n const MAX_PLANES = 40;\n const planes: { g: Vector; offset: number }[] = [...best.values()]\n .sort((a, b) => a.length2 - b.length2)\n .slice(0, MAX_PLANES)\n .map(({ g }) => ({ g, offset: dot(g, g) / 2 }));\n\n // Candidate BZ corners: intersections of three planes inside all planes\n const tolerance = 1e-10;\n const corners: Vector[] = [];\n const n = planes.length;\n for (let i = 0; i < n; i++) {\n for (let j = i + 1; j < n; j++) {\n for (let k = j + 1; k < n; k++) {\n const v = solve3(\n [planes[i].g, planes[j].g, planes[k].g],\n [planes[i].offset, planes[j].offset, planes[k].offset],\n tolerance,\n );\n if (!v) continue;\n let inside = true;\n for (const p of planes) {\n if (dot(p.g, v) > p.offset + tolerance) {\n inside = false;\n break;\n }\n }\n if (inside) corners.push(v);\n }\n }\n }\n\n // Deduplicate the corners\n const cornerMap: Map<string, Vector> = new Map();\n for (const v of corners) {\n const key = vertexKey(v);\n if (!cornerMap.has(key)) cornerMap.set(key, v);\n }\n const vertices = [...cornerMap.values()];\n\n // Group the corners that lie on each face plane; the face of the BZ is a\n // convex polygon of these coplanar vertices\n const faces: Vector[][] = [];\n const triangles: number[][] = [];\n const trianglesVertices: Vector[] = [];\n const vertexIndex: Map<string, number> = new Map();\n\n const addVertex = (v: Vector): number => {\n const key = vertexKey(v);\n let idx = vertexIndex.get(key);\n if (idx === undefined) {\n idx = trianglesVertices.length;\n vertexIndex.set(key, idx);\n trianglesVertices.push(v);\n }\n return idx;\n };\n\n for (const p of planes) {\n const on = vertices.filter(\n (v) => Math.abs(dot(p.g, v) - p.offset) < 1e-6,\n );\n if (on.length < 3) continue;\n\n // Sort the coplanar vertices angularly around the face centroid\n const centroid = [\n on.reduce((s, v) => s + v[0], 0) / on.length,\n on.reduce((s, v) => s + v[1], 0) / on.length,\n on.reduce((s, v) => s + v[2], 0) / on.length,\n ];\n const gx = Math.abs(p.g[0]);\n const gy = Math.abs(p.g[1]);\n const gz = Math.abs(p.g[2]);\n const ref =\n gx <= gy && gx <= gz\n ? new Float64Array([1, 0, 0])\n : gy <= gz\n ? new Float64Array([0, 1, 0])\n : new Float64Array([0, 0, 1]);\n let e1 = cross(p.g, ref);\n const e1Norm = norm(e1);\n e1 = new Float64Array([e1[0] / e1Norm, e1[1] / e1Norm, e1[2] / e1Norm]);\n const e2 = cross(p.g, e1);\n\n const ordered = [...on].sort((a, b) => {\n const da = new Float64Array([\n a[0] - centroid[0],\n a[1] - centroid[1],\n a[2] - centroid[2],\n ]);\n const db = new Float64Array([\n b[0] - centroid[0],\n b[1] - centroid[1],\n b[2] - centroid[2],\n ]);\n const angleA = Math.atan2(dot(da, e2), dot(da, e1));\n const angleB = Math.atan2(dot(db, e2), dot(db, e1));\n return angleA - angleB;\n });\n\n faces.push(ordered);\n\n // Fan triangulation of the face\n const first = addVertex(ordered[0]);\n for (let m = 1; m < ordered.length - 1; m++) {\n triangles.push([first, addVertex(ordered[m]), addVertex(ordered[m + 1])]);\n }\n }\n\n return {\n triangles_vertices: trianglesVertices.map((v) => Array.from(v)),\n triangles,\n faces: faces.map((face) => face.map((v) => Array.from(v))),\n };\n}\n","// prettier-ignore\n/** Space group data array indexed by space group number: [bravais_letter, centering, chiral]. /\nexport const spgroup_data: ([string, string, boolean] \| null)[] = [\n null, // unused (SG = 0)\n [\"a\",\"P\", false], [\"a\",\"P\", true], [\"m\",\"P\", false], [\"m\",\"P\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", false], [\"m\",\"P\", false], [\"m\",\"C\", false], \n [\"m\",\"C\", false], [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], \n [\"m\",\"P\", true], [\"m\",\"P\", true], [\"m\",\"C\", true], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], \n [\"o\",\"C\", false], [\"o\",\"F\", false], [\"o\",\"I\", false], [\"o\",\"I\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], \n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"P\", false],\n [\"o\",\"P\", false], [\"o\",\"P\", false], [\"o\",\"C\", false], [\"o\",\"C\", false],\n [\"o\",\"C\", false], [\"o\",\"A\", false], [\"o\",\"A\", false], [\"o\",\"A\", false],\n [\"o\",\"A\", false], [\"o\",\"F\", false], [\"o\",\"F\", false], [\"o\",\"I\", false],\n [\"o\",\"I\", false], [\"o\",\"I\", false], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], \n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"P\", true],\n [\"o\",\"P\", true], [\"o\",\"P\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true], [\"o\",\"C\", true],\n [\"o\",\"F\", true], [\"o\",\"F\", true], [\"o\",\"I\", true], [\"o\",\"I\", true],\n [\"o\",\"I\", true], [\"o\",\"I\", true], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false],\n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"P\", false], \n [\"t\",\"P\", false], [\"t\",\"P\", false], [\"t\",\"I\", false], [\"t\",\"I\", false],\n [\"t\",\"I\", false], [\"t\",\"I\", false], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], \n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"P\", true],\n [\"t\",\"P\", true], [\"t\",\"P\", true], [\"t\",\"I\", true], [\"t\",\"I\", true],\n [\"t\",\"I\", true], [\"t\",\"I\", true], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"R\", true],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"R\", false], \n [\"h\",\"R\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", true], [\"h\",\"R\", true], [\"h\",\"R\", true], [\"h\",\"P\", false],\n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", false], \n [\"h\",\"P\", false], [\"h\",\"P\", false], [\"h\",\"P\", true], [\"h\",\"P\", true],\n [\"h\",\"P\", true], [\"h\",\"P\", true], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", true],\n [\"c\",\"P\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"I\", true], \n [\"c\",\"P\", true], [\"c\",\"I\", true], [\"c\",\"P\", false], [\"c\",\"P\", false], \n [\"c\",\"F\", false], [\"c\",\"F\", false], [\"c\",\"I\", false], [\"c\",\"P\", false],\n [\"c\",\"P\", false], [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false],\n [\"c\",\"I\", false], [\"c\",\"P\", false], [\"c\",\"F\", false], [\"c\",\"I\", false],\n [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true], [\"c\",\"P\", true],\n [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], [\"c\",\"F\", true], \n [\"c\",\"I\", true], [\"c\",\"I\", true]];\n\n// prettier-ignore\n/* Centering symbols for each space group (1-indexed). /\nexport const centering: string[] = [\n \"P\",\"P\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"C\",\"P\",\"P\",\"P\",\n \"P\",\"C\",\"C\",\"F\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\n \"C\",\"A\",\"A\",\"A\",\"A\",\"F\",\"F\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"C\",\"C\",\"C\",\"C\",\"C\",\"C\",\"F\",\"F\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"I\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\n \"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"I\",\"I\",\"I\",\"I\",\"P\",\"P\",\n \"P\",\"R\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"R\",\"P\",\"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\n \"P\",\"P\",\"P\",\"R\",\"R\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\n \"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"P\",\"F\",\"I\",\"P\",\n \"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"I\",\"P\",\"P\",\"F\",\"F\",\"I\",\"P\",\"P\",\"I\",\"P\",\"F\",\n \"I\",\"P\",\"F\",\"I\",\"P\",\"P\",\"P\",\"P\",\"F\",\"F\",\"F\",\"F\",\"I\",\"I\"];\n","/\n Niggli reduction of a lattice basis.\n \n Produces the unique, canonical (Niggli) cell of a 3D lattice. The lattice is\n * given as a 3×3 matrix whose rows are the lattice vectors. The result is a\n * reduced basis spanning the same lattice, together with the unimodular\n * transformation matrix `T` such that `reduced = T × original` (row vectors).\n \n Unlike LLL (which returns a short basis), Niggli reduction is a\n * normalization: its result is unique, which is why seekpath and\n * crystallography use it (e.g. to canonicalise the triclinic aP cell).\n \n This is a faithful port of spglib's `niggli_reduce` (Grosse-Kunstleve\n * 8-step algorithm), using the same `eps` tolerance semantics. The exported\n * `niggli` operates on row-vector bases and produces output matching spglib's\n * `niggli_reduce` for the same row-major lattice array.\n \n The iteration is hand-unrolled: no step-transform matrices are materialised\n * and no generic 3×3 matrix multiplication runs in the hot path. Each step is\n * a sparse in-place row operation on the basis (a permutation/sign-flip or a\n * single-row shear), which is far cheaper than a general matmul.\n \n The basis is kept in the same row-vector arrangement as the public API, so\n * no transposition is ever needed: the input is reduced in place and returned\n * directly. The Gram matrix is symmetric, so the metric and its analytic\n * updates are identical whether the vectors are treated as rows or columns;\n * only the orientation of the sparse in-place mutations differs.\n \n @see https://github.com/spglib/spglib/blob/master/src/niggli.c\n /\n\nimport { Matrix } from \"../../matrix\";\n\ninterface KernelOut {\n l: number;\n m: number;\n n: number;\n ok: boolean;\n}\n\nfunction niggliKernel(\n input: Float64Array,\n basis: Float64Array,\n transform: Float64Array \| null,\n eps: number,\n out: KernelOut,\n): void {\n const r = transform;\n\n // Scalarized 3×3 basis (rows are lattice vectors). Operated on directly and\n // written back to `basis` only once the reduction converges.\n let b00 = input[0];\n let b01 = input[1];\n let b02 = input[2];\n let b10 = input[3];\n let b11 = input[4];\n let b12 = input[5];\n let b20 = input[6];\n let b21 = input[7];\n let b22 = input[8];\n\n // Scalarized accumulated unimodular transform T (starts as identity). The\n // same sparse row ops applied to the basis are applied here, so at the end\n // reduced = T × original. Written back to `transform` only at the end.\n let x00 = r ? r[0] : 1;\n let x01 = r ? r[1] : 0;\n let x02 = r ? r[2] : 0;\n let x10 = r ? r[3] : 0;\n let x11 = r ? r[4] : 1;\n let x12 = r ? r[5] : 0;\n let x20 = r ? r[6] : 0;\n let x21 = r ? r[7] : 0;\n let x22 = r ? r[8] : 1;\n\n // --- Initial metric parameters ---\n let A = b00 b00 + b01 * b01 + b02 * b02;\n let B = b10 * b10 + b11 * b11 + b12 * b12;\n let C = b20 * b20 + b21 * b21 + b22 * b22;\n let zeta = 2 * (b00 * b10 + b01 * b11 + b02 * b12);\n let eta = 2 * (b00 * b20 + b01 * b21 + b02 * b22);\n let xi = 2 * (b10 * b20 + b11 * b21 + b12 * b22);\n\n let l = 0;\n let m = 0;\n let n = 0;\n\n const maxAttempts = 1000;\n for (let attempt = 0; attempt < maxAttempts; attempt++) {\n // ---- Step 1: r0 = −r1, r1 = −r0, r2 = −r2 ----\n // (A,B,C,xi,eta,zeta) -> (B,A,C,eta,xi,zeta)\n if (A > B + eps \|\| (Math.abs(A - B) <= eps && Math.abs(xi) > Math.abs(eta) + eps)) {\n let t00 = b00;\n b00 = -b10; b10 = -t00;\n let t01 = b01;\n b01 = -b11; b11 = -t01;\n let t02 = b02;\n b02 = -b12; b12 = -t02;\n b20 = -b20; b21 = -b21; b22 = -b22;\n let xt00 = x00;\n x00 = -x10; x10 = -xt00;\n let xt01 = x01;\n x01 = -x11; x11 = -xt01;\n let xt02 = x02;\n x02 = -x12; x12 = -xt02;\n x20 = -x20; x21 = -x21; x22 = -x22;\n const tA = A;\n const txi = xi;\n A = B;\n B = tA;\n xi = eta;\n eta = txi;\n }\n\n // ---- Step 2: r0 = −r0, r1 = −r2, r2 = −r1 ----\n // (A,B,C,xi,eta,zeta) -> (A,C,B,xi,zeta,eta)\n if (B > C + eps \|\| (Math.abs(B - C) <= eps && Math.abs(eta) > Math.abs(zeta) + eps)) {\n b00 = -b00; b01 = -b01; b02 = -b02;\n let t0 = b10;\n b10 = -b20; b20 = -t0;\n let t1 = b11;\n b11 = -b21; b21 = -t1;\n let t2 = b12;\n b12 = -b22; b22 = -t2;\n x00 = -x00; x01 = -x01; x02 = -x02;\n let xt0 = x10;\n x10 = -x20; x20 = -xt0;\n let xt1 = x11;\n x11 = -x21; x21 = -xt1;\n let xt2 = x12;\n x12 = -x22; x22 = -xt2;\n const tB = B;\n const teta = eta;\n B = C;\n C = tB;\n eta = zeta;\n zeta = teta;\n continue;\n }\n\n // ---- Step 3: sign flip so l·m·n = 1 ----\n l = xi < -eps ? -1 : xi > eps ? 1 : 0;\n m = eta < -eps ? -1 : eta > eps ? 1 : 0;\n n = zeta < -eps ? -1 : zeta > eps ? 1 : 0;\n const lmn = l * m * n;\n if (lmn === 1) {\n const i = l === -1 ? -1 : 1;\n const j = m === -1 ? -1 : 1;\n const k = n === -1 ? -1 : 1;\n b00 = i; b01 = i; b02 = i;\n b10 = j; b11 = j; b12 = j;\n b20 = k; b21 = k; b22 = k;\n x00 = i; x01 = i; x02 = i;\n x10 = j; x11 = j; x12 = j;\n x20 = k; x21 = k; x22 = k;\n zeta = i j;\n eta = i k;\n xi = j k;\n }\n\n // ---- Step 4: further sign flips when l·m·n ∈ {0, −1} ----\n if (!(l === -1 && m === -1 && n === -1)) {\n if (lmn === 0 \|\| lmn === -1) {\n let i = 1;\n let j = 1;\n let k = 1;\n let which = -1;\n if (l === 1) i = -1;\n if (l === 0) which = 0;\n if (m === 1) j = -1;\n if (m === 0) which = 1;\n if (n === 1) k = -1;\n if (n === 0) which = 2;\n\n if (i * j * k === -1) {\n if (which === 0) i = -1;\n if (which === 1) j = -1;\n if (which === 2) k = -1;\n }\n\n b00 = i; b01 = i; b02 = i;\n b10 = j; b11 = j; b12 = j;\n b20 = k; b21 = k; b22 = k;\n x00 = i; x01 = i; x02 = i;\n x10 = j; x11 = j; x12 = j;\n x20 = k; x21 = k; x22 = k;\n zeta = i j;\n eta = i k;\n xi = j k;\n }\n }\n\n // ---- Step 5: r2 += sign · r1 ----\n if (\n Math.abs(xi) > B + eps \|\|\n (Math.abs(B - xi) <= eps && 2 * eta < zeta - eps) \|\|\n (Math.abs(B + xi) <= eps && zeta < -eps)\n ) {\n const s: number = xi > 0 ? -1 : 1;\n b20 += s * b10; b21 += s * b11; b22 += s * b12;\n x20 += s * x10; x21 += s * x11; x22 += s * x12;\n C += s * xi + B;\n xi = xi + 2 * s * B;\n eta = eta + s * zeta;\n continue;\n }\n\n // ---- Step 6: r2 += sign · r0 ----\n if (\n Math.abs(eta) > A + eps \|\|\n (Math.abs(A - eta) <= eps && 2 * xi < zeta - eps) \|\|\n (Math.abs(A + eta) <= eps && zeta < -eps)\n ) {\n const s: number = eta > 0 ? -1 : 1;\n b20 += s * b00; b21 += s * b01; b22 += s * b02;\n x20 += s * x00; x21 += s * x01; x22 += s * x02;\n C += s * eta + A;\n xi = xi + s * zeta;\n eta = eta + 2 * s * A;\n continue;\n }\n\n // ---- Step 7: r1 += sign · r0 ----\n if (\n Math.abs(zeta) > A + eps \|\|\n (Math.abs(A - zeta) <= eps && 2 * xi < eta - eps) \|\|\n (Math.abs(A + zeta) <= eps && eta < -eps)\n ) {\n const s: number = zeta > 0 ? -1 : 1;\n b10 += s * b00; b11 += s * b01; b12 += s * b02;\n x10 += s * x00; x11 += s * x01; x12 += s * x02;\n B += s * zeta + A;\n xi = xi + s * eta;\n zeta = zeta + 2 * s * A;\n continue;\n }\n\n // ---- Step 8: r2 += r0 + r1 ----\n {\n const sum = xi + eta + zeta + A + B;\n if (\n sum < -eps \|\|\n (Math.abs(sum) <= eps && 2 * (A + eta) + zeta > eps)\n ) {\n b20 += b00 + b10; b21 += b01 + b11; b22 += b02 + b12;\n x20 += x00 + x10; x21 += x01 + x11; x22 += x02 + x12;\n C += A + B + xi + eta + zeta;\n xi = xi + zeta + 2 * B;\n eta = eta + zeta + 2 * A;\n continue;\n }\n }\n\n // No step fired: converged.\n out.l = l;\n out.m = m;\n out.n = n;\n out.ok = true;\n basis[0] = b00; basis[1] = b01; basis[2] = b02;\n basis[3] = b10; basis[4] = b11; basis[5] = b12;\n basis[6] = b20; basis[7] = b21; basis[8] = b22;\n if (r) {\n r[0] = x00; r[1] = x01; r[2] = x02;\n r[3] = x10; r[4] = x11; r[5] = x12;\n r[6] = x20; r[7] = x21; r[8] = x22;\n }\n return;\n }\n\n basis[0] = b00; basis[1] = b01; basis[2] = b02;\n basis[3] = b10; basis[4] = b11; basis[5] = b12;\n basis[6] = b20; basis[7] = b21; basis[8] = b22;\n if (r) {\n r[0] = x00; r[1] = x01; r[2] = x02;\n r[3] = x10; r[4] = x11; r[5] = x12;\n r[6] = x20; r[7] = x21; r[8] = x22;\n }\n out.ok = false;\n}\n\nexport interface NiggliResult {\n /** The Niggli-reduced basis (3×3, rows are lattice vectors). /\n basis: Matrix;\n /\n The unimodular transformation matrix `T` such that\n * `reduced = T × original` (row-vector convention).\n /\n transform: Matrix;\n}\n\n/\n Reduce a 3×3 lattice basis (rows = lattice vectors) to its unique Niggli\n * cell.\n \n @param input A 3×3 matrix whose rows are the lattice vectors.\n * @param eps Tolerance against which near-equalities are decided. Mirrors\n * spglib's `symprec` (default `1e-5`).\n * @returns The reduced basis and transformation, or `null` if reduction did\n * not converge.\n /\nexport function niggli(input: Matrix, eps = 1e-5): NiggliResult \| null {\n if (input.rows !== 3 \|\| input.cols !== 3) {\n throw new Error(\n `niggli requires a 3x3 matrix, got ${input.rows}×${input.cols}`,\n );\n }\n\n // The basis is kept in row-vector form throughout (rows are the lattice\n // vectors), so the input is reduced directly and the result returned as-is;\n // no transposition is needed. `rightTransform` accumulates the same row\n // operations, yielding directly the left-multiply form `reduced = T × input`.\n const basis = new Float64Array(input.data);\n const transform = new Float64Array([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n const out: KernelOut = { l: 0, m: 0, n: 0, ok: false };\n niggliKernel(input.data, basis, transform, eps, out);\n if (!out.ok) return null;\n\n // `basis` is a private working copy (never the caller's input) and\n // `transform` is integer-valued, so wrap them directly as the result\n // matrices without an extra array copy.\n return {\n basis: { rows: 3, cols: 3, data: basis },\n transform: { rows: 3, cols: 3, data: transform },\n };\n}\n","import { Matrix, createMatrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { scale } from \"@/core/matrix/operations/scale\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\n\nconst TWO_PI = 2 Math.PI;\n\n/** Build a 3x3 Matrix from 9 row-major values. /\nexport function matrixFromRowMajor(data: ArrayLike<number>): Matrix {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return createMatrix(3, 3, Array.from(data));\n}\n\n/\n Return [a, b, c, cosalpha, cosbeta, cosgamma] for a 3x3 lattice whose\n * rows are the lattice vectors.\n /\nexport function cellParams(\n lattice: Matrix,\n): [number, number, number, number, number, number] {\n const d = lattice.data;\n const v1 = [d[0], d[1], d[2]];\n const v2 = [d[3], d[4], d[5]];\n const v3 = [d[6], d[7], d[8]];\n const a = Math.hypot(v1[0], v1[1], v1[2]);\n const b = Math.hypot(v2[0], v2[1], v2[2]);\n const c = Math.hypot(v3[0], v3[1], v3[2]);\n const dot = (u: number[], v: number[]) =>\n u[0] v[0] + u[1] * v[1] + u[2] * v[2];\n const cosalpha = dot(v2, v3) / b / c;\n const cosbeta = dot(v1, v3) / a / c;\n const cosgamma = dot(v1, v2) / a / b;\n return [a, b, c, cosalpha, cosbeta, cosgamma];\n}\n\n/** Reciprocal-space cell rows, such that dot(real, recip.T) = 2π I. /\nexport function getReciprocalCellRows(real: Matrix): Matrix {\n return transpose(scale(gjInverse(real), TWO_PI));\n}\n\n/* Real-space cell rows given reciprocal rows, such that dot(recip, real.T) = 2π I. /\nexport function getRealCellFromReciprocalRows(recip: Matrix): Matrix {\n return transpose(scale(gjInverse(recip), TWO_PI));\n}\n\n/\n Return the (P, invP) transformation matrices from the crystallographic\n * conventional cell to the primitive cell, as in Table 3 of the HPKOT paper:\n * (a_P, b_P, c_P) = (a, b, c) P and (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T.\n /\nexport function getPmatrix(\n bravaisLattice: string,\n): { P: number[][]; invP: number[][] } {\n if ([\"cP\", \"tP\", \"hP\", \"oP\", \"mP\"].includes(bravaisLattice)) {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if ([\"cF\", \"oF\"].includes(bravaisLattice)) {\n return {\n P: [\n [0, 0.5, 0.5],\n [0.5, 0, 0.5],\n [0.5, 0.5, 0],\n ],\n invP: [\n [-1, 1, 1],\n [1, -1, 1],\n [1, 1, -1],\n ],\n };\n }\n if ([\"cI\", \"tI\", \"oI\"].includes(bravaisLattice)) {\n return {\n P: [\n [-0.5, 0.5, 0.5],\n [0.5, -0.5, 0.5],\n [0.5, 0.5, -0.5],\n ],\n invP: [\n [0, 1, 1],\n [1, 0, 1],\n [1, 1, 0],\n ],\n };\n }\n if (bravaisLattice === \"hR\") {\n return {\n P: [\n [2 / 3, -1 / 3, -1 / 3],\n [1 / 3, 1 / 3, -2 / 3],\n [1 / 3, 1 / 3, 1 / 3],\n ],\n invP: [\n [1, 0, 1],\n [-1, 1, 1],\n [0, -1, 1],\n ],\n };\n }\n if (bravaisLattice === \"oC\") {\n return {\n P: [\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, -1, 0],\n [1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"oA\") {\n return {\n P: [\n [0, 0, 1],\n [0.5, 0.5, 0],\n [-0.5, 0.5, 0],\n ],\n invP: [\n [0, 1, -1],\n [0, 1, 1],\n [1, 0, 0],\n ],\n };\n }\n if (bravaisLattice === \"mC\") {\n return {\n P: [\n [0.5, -0.5, 0],\n [0.5, 0.5, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 1, 0],\n [-1, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n if (bravaisLattice === \"aP\") {\n return {\n P: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n invP: [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n };\n }\n throw new Error(`Invalid bravais_lattice ${bravaisLattice}`);\n}\n\nexport interface PrimitiveCellResult {\n lattice: number[][];\n positions: number[][];\n types: number[];\n mapping: number[];\n}\n\n/\n Build the crystallographic primitive cell from a standardized conventional\n * cell using the HPKOT P matrices, deduplicating atoms that coincide modulo 1.\n /\nexport function getPrimitive(\n lattice: number[][],\n positions: number[][],\n types: number[],\n bravaisLattice: string,\n threshold = 1e-6,\n): PrimitiveCellResult {\n const { P, invP } = getPmatrix(bravaisLattice);\n\n const volumeRatio = Math.round(Math.abs(det3(invP)));\n\n // (a_P, b_P, c_P) = (a, b, c) P => prim vector j = sum_k P[k][j] a_k,\n // i.e. prim_lattice = P^T @ lattice\n const primLattice = matmul3(transpose3(P), lattice);\n // (x_P, y_P, z_P)^T = P^-1 (x, y, z)^T => row-vector form: positions @ invP.T\n const primPositions = matmul3(positions, transpose3(invP));\n\n const n = positions.length;\n\n // Mark equivalent atoms (same position modulo 1, shifted so that ±0.5 wrap)\n const match = (u: number, v: number) => {\n const diff = Math.abs(((u - v + 0.5) % 1 + 1) % 1 - 0.5);\n return diff < threshold;\n };\n\n const groups: number[][] = [];\n const assigned = new Array<boolean>(n).fill(false);\n\n for (let i = 0; i < n; i++) {\n if (assigned[i]) continue;\n const group: number[] = [];\n for (let j = i; j < n; j++) {\n if (\n match(primPositions[j][0], primPositions[i][0]) &&\n match(primPositions[j][1], primPositions[i][1]) &&\n match(primPositions[j][2], primPositions[i][2])\n ) {\n group.push(j);\n assigned[j] = true;\n }\n }\n groups.push(group);\n }\n\n for (const group of groups) {\n if (group.length !== volumeRatio) {\n throw new Error(\n `Problem creating primitive cell, found group of atoms with length ${group.length} != ${volumeRatio}`,\n );\n }\n const typeSet = new Set(group.map((idx) => types[idx]));\n if (typeSet.size !== 1) {\n throw new Error(\n \"The following atoms go on top of each other, but they are of different type!\",\n );\n }\n }\n\n groups.sort((a, b) => a[0] - b[0]);\n\n const mapping = new Array<number>(n).fill(-1);\n for (let primIdx = 0; primIdx < groups.length; primIdx++) {\n for (const atIdx of groups[primIdx]) mapping[atIdx] = primIdx;\n }\n\n return {\n lattice: primLattice,\n positions: groups.map((g) => primPositions[g[0]]),\n types: groups.map((g) => types[g[0]]),\n mapping,\n };\n}\n\nfunction transpose3(m: number[][]): number[][] {\n return [\n [m[0][0], m[1][0], m[2][0]],\n [m[0][1], m[1][1], m[2][1]],\n [m[0][2], m[1][2], m[2][2]],\n ];\n}\n\nfunction matmul3(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] * b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nfunction det3(m: number[][]): number {\n return (\n m[0][0] * (m[1][1] * m[2][2] - m[1][2] * m[2][1]) -\n m[0][1] * (m[1][0] * m[2][2] - m[1][2] * m[2][0]) +\n m[0][2] * (m[1][0] * m[2][1] - m[1][1] * m[2][0])\n );\n}\n\n/** Evaluate an expression that only requires precomputed k-parameters. /\nexport function evalExprSimple(expr: string, kparam: Record<string, number>): number {\n switch (expr) {\n case \"0\":\n return 0;\n case \"1/2\":\n return 0.5;\n case \"1\":\n return 1;\n case \"-1/2\":\n return -0.5;\n case \"1/4\":\n return 0.25;\n case \"3/8\":\n return 0.375;\n case \"3/4\":\n return 0.75;\n case \"5/8\":\n return 0.625;\n case \"1/3\":\n return 1 / 3;\n default: {\n const val = kparam[expr];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${expr}' in eval_expr_simple but this has not been defined or not yet computed`,\n );\n }\n return val;\n }\n }\n}\n\n/* Extend kparam with derived expressions (1-x, -x, 1/2-x, ...). /\nexport function extendKparam(kparam: Record<string, number>): Record<string, number> {\n const extended: Record<string, number> = {};\n for (const [key, val] of Object.entries(kparam)) {\n extended[key] = val;\n extended[`-${key}`] = -val;\n extended[`1-${key}`] = 1 - val;\n extended[`-1+${key}`] = -1 + val;\n extended[`1/2-${key}`] = 0.5 - val;\n extended[`1/2+${key}`] = 0.5 + val;\n }\n return extended;\n}\n\n/\n Evaluate a k-parameter expression as a function of the cell parameters and\n * previously computed k-parameters. Mirrors the hardcoded table in seekpath.\n /\nexport function evalExpr(\n expr: string,\n a: number,\n b: number,\n c: number,\n cosalpha: number,\n cosbeta: number,\n cosgamma: number,\n kparam: Record<string, number>,\n): number {\n const sinbeta = Math.sqrt(1 - cosbeta cosbeta);\n\n const k = (name: string): number => {\n const val = kparam[name];\n if (val === undefined) {\n throw new Error(\n `Asking for evaluation of symbol '${name}' but this has not been defined or not yet computed`,\n );\n }\n return val;\n };\n const Z = () => k(\"Z\");\n const E = () => k(\"E\");\n const F = () => k(\"F\");\n const U = () => k(\"U\");\n const W = () => k(\"W\");\n const S = () => k(\"S\");\n const M = () => k(\"M\");\n const X = () => k(\"X\");\n const D = () => k(\"D\");\n const Y = () => k(\"Y\");\n\n switch (expr) {\n case \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\":\n return (a * a / b / b + (1 + a / c * cosbeta) / sinbeta / sinbeta) / 4;\n case \"1-Zbb/a/a\":\n return 1 - Z() * b * b / a / a;\n case \"1/2-2Zccosbeta/a\":\n return 0.5 - 2 Z() * c * cosbeta / a;\n case \"E/2+aa/4/b/b+accosbeta/2/b/b\":\n return E() / 2 + a a / 4 / b / b + a * c * cosbeta / 2 / b / b;\n case \"2F-Z\":\n return 2 F() - Z();\n case \"c/2/a/cosbeta(1-4U+aasinbetasinbeta/b/b)\":\n return (\n c / 2 / a / cosbeta (1 - 4 * U() + a * a * sinbeta * sinbeta / b / b)\n );\n case \"-1/4+W/2-Zccosbeta/a\":\n return -0.25 + W() / 2 - Z() * c * cosbeta / a;\n case \"(2+a/ccosbeta)/4/sinbeta/sinbeta\":\n return (2 + a / c cosbeta) / 4 / sinbeta / sinbeta;\n case \"3/4-bb/4/a/a/sinbeta/sinbeta\":\n return 3 / 4 - b b / 4 / a / a / sinbeta / sinbeta;\n case \"S-(3/4-S)acosbeta/c\":\n return S() - (3 / 4 - S()) * a * cosbeta / c;\n case \"(1+aa/b/b)/4\":\n return (1 + a a / b / b) / 4;\n case \"-accosbeta/2/b/b\":\n return -a * c * cosbeta / 2 / b / b;\n case \"1+Z-2M\":\n return 1 + Z() - 2 M();\n case \"X-2D\":\n return X() - 2 D();\n case \"(1+a/ccosbeta)/2/sinbeta/sinbeta\":\n return (1 + a / c cosbeta) / 2 / sinbeta / sinbeta;\n case \"1/2+Yccosbeta/a\":\n return 0.5 + Y() * c * cosbeta / a;\n case \"aa/4/c/c\":\n return a a / 4 / c / c;\n case \"5/6-2D\":\n return 5 / 6 - 2 D();\n case \"1/3+D\":\n return 1 / 3 + D();\n case \"1/6-cc/9/a/a\":\n return 1 / 6 - c c / 9 / a / a;\n case \"1/2-2Z\":\n return 0.5 - 2 Z();\n case \"1/2+Z\":\n return 0.5 + Z();\n case \"(1+bb/c/c)/4\":\n return (1 + b b / c / c) / 4;\n case \"(1+cc/b/b)/4\":\n return (1 + c c / b / b) / 4;\n case \"(1+bb/a/a)/4\":\n return (1 + b b / a / a) / 4;\n case \"(1+aa/b/b-aa/c/c)/4\":\n return (1 + a * a / b / b - a * a / c / c) / 4;\n case \"(1+aa/b/b+aa/c/c)/4\":\n return (1 + a * a / b / b + a * a / c / c) / 4;\n case \"(1+cc/a/a-cc/b/b)/4\":\n return (1 + c * c / a / a - c * c / b / b) / 4;\n case \"(1+cc/a/a+cc/b/b)/4\":\n return (1 + c * c / a / a + c * c / b / b) / 4;\n case \"(1+bb/a/a-bb/c/c)/4\":\n return (1 + b * b / a / a - b * b / c / c) / 4;\n case \"(1+cc/b/b-cc/a/a)/4\":\n return (1 + c * c / b / b - c * c / a / a) / 4;\n case \"(1+aa/c/c)/4\":\n return (1 + a a / c / c) / 4;\n case \"(bb-aa)/4/c/c\":\n return (b * b - a * a) / 4 / c / c;\n case \"(aa+bb)/4/c/c\":\n return (a * a + b * b) / 4 / c / c;\n case \"(1+cc/a/a)/4\":\n return (1 + c c / a / a) / 4;\n case \"(cc-bb)/4/a/a\":\n return (c * c - b * b) / 4 / a / a;\n case \"(bb+cc)/4/a/a\":\n return (b * b + c * c) / 4 / a / a;\n case \"(aa-cc)/4/b/b\":\n return (a * a - c * c) / 4 / b / b;\n case \"(cc+aa)/4/b/b\":\n return (c * c + a * a) / 4 / b / b;\n case \"aa/2/c/c\":\n return a a / 2 / c / c;\n default:\n throw new Error(\n `Unknown expression, define a new case: '${expr}'`,\n );\n }\n}\n\n/** Wrap a cell in a Matrix to use matrix helpers. /\nexport function toMatrix(rows: number[][]): Matrix {\n return createMatrix(3, 3, rows.flat());\n}\n\n/* Row-vector times matrix: x_abs[i] = v . col_i(m). /\nexport function vecMulMat(v: readonly number[], m: number[][]): number[] {\n return [\n v[0] m[0][0] + v[1] * m[1][0] + v[2] * m[2][0],\n v[0] * m[0][1] + v[1] * m[1][1] + v[2] * m[2][1],\n v[0] * m[0][2] + v[1] * m[1][2] + v[2] * m[2][2],\n ];\n}\n","import { Matrix } from \"@/core/matrix/matrix\";\nimport { transpose } from \"@/core/matrix/operations/transpose\";\nimport { mul } from \"@/core/matrix/operations/mul\";\nimport { gjInverse } from \"@/core/matrix/operations/inverse/gaussJordan\";\nimport { niggli } from \"@/core/matrix/operations/reduction/niggli\";\nimport {\n cellParams,\n getReciprocalCellRows,\n getRealCellFromReciprocalRows,\n matrixFromRowMajor,\n} from \"./seekpathTools\";\n\nconst M2_MATRICES = [\n [\n [0, 0, 1],\n [1, 0, 0],\n [0, 1, 0],\n ],\n [\n [0, 1, 0],\n [0, 0, 1],\n [1, 0, 0],\n ],\n [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ],\n];\n\n/** Determine the aP label (aP2 all-obtuse / aP3 all-acute) as in HPKOT. /\nconst M3_I = [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n];\nconst M3_XX = [\n [1, 0, 0],\n [0, -1, 0],\n [0, 0, -1],\n];\nconst M3_YY = [\n [-1, 0, 0],\n [0, 1, 0],\n [0, 0, -1],\n];\nconst M3_ZZ = [\n [-1, 0, 0],\n [0, -1, 0],\n [0, 0, 1],\n];\n\nfunction mulRows(a: number[][], b: number[][]): number[][] {\n const out: number[][] = [];\n for (let i = 0; i < a.length; i++) {\n const row: number[] = [];\n for (let j = 0; j < b[0].length; j++) {\n let sum = 0;\n for (let k = 0; k < b.length; k++) sum += a[i][k] b[k][j];\n row.push(sum);\n }\n out.push(row);\n }\n return out;\n}\n\nexport interface APTransform {\n lattice: number[][];\n positions: number[][];\n extBravais: string;\n}\n\n/*\n Apply the Niggli reduction plus the M2/M3 vector transforms of the HPKOT\n * paper to bring a triclinic conventional cell into the all-obtuse (aP2) or\n * all-acute (aP3) setting.\n /\nexport async function transformAP(\n lattice: number[][],\n positions: number[][],\n): Promise<APTransform> {\n const convLattice = matrixFromRowMajor(lattice.flat());\n\n const reciprocalCellOrig = getReciprocalCellRows(convLattice);\n const reduced = niggli(reciprocalCellOrig);\n if (!reduced) throw new Error(\"Niggli reduction failed for aP lattice\");\n const reciprocalCell2 = reduced.basis;\n const realCell2 = getRealCellFromReciprocalRows(reciprocalCell2);\n\n const [ka2, kb2, kc2, coskalpha2, coskbeta2, coskgamma2] =\n cellParams(reciprocalCell2);\n const conditions = [\n Math.abs(kb2 kc2 * coskalpha2),\n Math.abs(kc2 * ka2 * coskbeta2),\n Math.abs(ka2 * kb2 * coskgamma2),\n ];\n\n let smallest = 0;\n if (conditions[1] < conditions[smallest]) smallest = 1;\n if (conditions[2] < conditions[smallest]) smallest = 2;\n const M2 = matrixFromRowMajor(M2_MATRICES[smallest].flat());\n const realCell3 = mul(transpose(M2), realCell2);\n\n const reciprocalCell3 = getReciprocalCellRows(realCell3);\n const [, , , ca3, cb3, cg3] = cellParams(reciprocalCell3);\n\n let M3: number[][];\n if ((ca3 > 0 && cb3 > 0 && cg3 > 0) \|\| (ca3 <= 0 && cb3 <= 0 && cg3 <= 0))\n M3 = M3_I;\n else if (\n (ca3 > 0 && cb3 <= 0 && cg3 <= 0) \|\|\n (ca3 <= 0 && cb3 > 0 && cg3 > 0)\n )\n M3 = M3_XX;\n else if (\n (ca3 <= 0 && cb3 > 0 && cg3 <= 0) \|\|\n (ca3 > 0 && cb3 <= 0 && cg3 > 0)\n )\n M3 = M3_YY;\n else if (\n (ca3 <= 0 && cb3 <= 0 && cg3 > 0) \|\|\n (ca3 > 0 && cb3 > 0 && cg3 <= 0)\n )\n M3 = M3_ZZ;\n else\n throw new Error(\n \"Problem identifying M3 matrix in aP lattice: sign pattern of cosines ambiguous\",\n );\n\n const M3mat = matrixFromRowMajor(M3.flat());\n const realCellFinal = mul(transpose(M3mat), realCell3);\n const reciprocalCellFinal = getReciprocalCellRows(realCellFinal);\n const [, , , ca, cb, cg] = cellParams(reciprocalCellFinal);\n\n let extBravais: string;\n if (ca <= 0 && cb <= 0 && cg <= 0) extBravais = \"aP2\";\n else if (ca >= 0 && cb >= 0 && cg >= 0) extBravais = \"aP3\";\n else\n throw new Error(\n \"Unexpected aP lattice, neither all-obtuse nor all-acute in reciprocal space\",\n );\n\n // Express the (absolute) atomic positions in the new real cell basis\n const finalRows = Array.from(realCellFinal.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const absPositions = mulRows(positions, lattice);\n const invFinal = gjInverse(matrixFromRowMajor(finalRows.flat()));\n const newPositions = absPositions.map((p) => {\n const v = createVector(p);\n const res = mul(invFinal, v).data;\n return [res[0], res[1], res[2]];\n });\n\n return {\n lattice: finalRows,\n positions: newPositions,\n extBravais,\n };\n}\n\nfunction createVector(v: number[]): Matrix {\n return { rows: 3, cols: 1, data: new Float64Array(v) };\n}\n\n/** Determine the aP label (aP2 / aP3) for a triclinic conventional lattice. /\nexport async function determineAP(convLattice: Matrix): Promise<string> {\n const rows = Array.from(convLattice.data).reduce<number[][]>(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n );\n const { extBravais } = await transformAP(rows, []);\n return extBravais;\n}\n\n/* Determine the Seekpath extended Bravais lattice from a conventional cell. /\nexport function determineExtBravais(\n bL: string,\n spgN: number,\n a: number,\n b: number,\n c: number,\n alpha: number,\n beta: number,\n gamma: number,\n): string {\n const threshold = 1e-7;\n\n switch (bL) {\n case \"cP\":\n if (spgN < 195 \|\| spgN > 230)\n throw new Error(\"cP requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cP1\" : \"cP2\";\n\n case \"cF\":\n if (spgN < 195 \|\| spgN > 230)\n throw new Error(\"cF requires spacegroup number in [195, 230]\");\n return spgN <= 206 ? \"cF1\" : \"cF2\";\n\n case \"cI\":\n return \"cI1\";\n\n case \"tP\":\n return \"tP1\";\n\n case \"tI\":\n if (c - a < threshold) {\n console.warn(\"tI lattice, a ≈ c\");\n }\n return c <= a ? \"tI1\" : \"tI2\";\n\n case \"oP\":\n return \"oP1\";\n\n case \"oF\": {\n const A = 1.0 / a * 2;\n const B = 1.0 / b 2;\n const C = 1.0 / c 2;\n\n if (A > B + C) {\n return \"oF1\";\n }\n\n if (C > A + B) {\n return \"oF2\";\n } else return \"oF3\";\n }\n\n case \"oI\": {\n const sorted = [\n { v: c, id: 1 },\n { v: b, id: 3 },\n { v: a, id: 2 },\n ]\n .sort((x, y) => x.v - y.v \|\| x.id - y.id)\n .reverse();\n\n if (Math.abs(sorted[0].v - sorted[1].v) < threshold) {\n console.warn(\"oI near-degeneracy\");\n }\n\n return `${bL}${sorted[0].id}`;\n }\n\n case \"oC\":\n return a <= b ? \"oC1\" : \"oC2\";\n\n case \"oA\":\n return b <= c ? \"oA1\" : \"oA2\";\n\n case \"hP\":\n return [\n 143, 144, 145, 146, 147, 148, 149, 151, 153, 157, 159, 160, 161, 162,\n 163,\n ].includes(spgN)\n ? \"hP1\"\n : \"hP2\";\n\n case \"hR\":\n return Math.sqrt(3) * a <= Math.sqrt(2) * c ? \"hR1\" : \"hR2\";\n\n case \"mP\":\n return \"mP1\";\n\n case \"mC\": {\n const rad = Math.PI / 180;\n const cosbeta = Math.cos(beta * rad);\n const sinbeta = Math.sin(beta * rad);\n\n const term1 = b - a * Math.sqrt(1 - cosbeta ** 2);\n\n if (Math.abs(term1) < threshold) {\n console.warn(\"mC near-degeneracy\");\n }\n\n if (b < a * sinbeta) return \"mC1\";\n\n const expr = (-a * cosbeta) / c + (a ** 2 * (1 - cosbeta 2)) / b 2;\n if (Math.abs(expr - 1.0) < threshold) {\n console.warn(\"mC second degeneracy\");\n }\n\n return expr <= 1 ? \"mC2\" : \"mC3\";\n }\n\n case \"aP\":\n throw new Error(\"aP must be handled by determineAP\");\n\n default:\n throw new Error(`Unknown bravais lattice: ${bL}`);\n }\n}\n","// AUTO-GENERATED FILE — DO NOT EDIT\n// Source: https://github.com/materialscloud-org/seekpath (HPKOT band path data)\n\nexport interface BandPathData {\n kparam: [string, string][];\n points: Record<string, [string, string, string]>;\n path: [string, string][];\n}\n\nexport const bandPathData: Record<string, BandPathData> = {\n \"aP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V\": [\"1/2\", \"1/2\", \"0\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"U\", \"GAMMA\"],\n [\"GAMMA\", \"V\"]\n ],\n },\n \"aP3\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"Y_2\": [\"0\", \"-1/2\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"1/2\", \"-1/2\", \"0\"],\n \"U_2\": [\"-1/2\", \"0\", \"1/2\"],\n \"T_2\": [\"0\", \"-1/2\", \"1/2\"],\n \"R_2\": [\"-1/2\", \"-1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"R_2\", \"GAMMA\"],\n [\"GAMMA\", \"T_2\"],\n [\"U_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"cF1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"],\n [\"X\", \"W_2\"]\n ],\n },\n \"cF2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"],\n \"W\": [\"1/2\", \"1/4\", \"3/4\"],\n \"W_2\": [\"3/4\", \"1/4\", \"1/2\"],\n \"K\": [\"3/8\", \"3/8\", \"3/4\"],\n \"U\": [\"5/8\", \"1/4\", \"5/8\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"L\"],\n [\"L\", \"W\"],\n [\"W\", \"X\"]\n ],\n },\n \"cI1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"H\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"H\"],\n [\"H\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"P\"],\n [\"P\", \"H\"],\n [\"P\", \"N\"]\n ],\n },\n \"cP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"],\n [\"M\", \"X_1\"]\n ],\n },\n \"cP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"X\": [\"0\", \"1/2\", \"0\"],\n \"X_1\": [\"1/2\", \"0\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"X\"],\n [\"R\", \"M\"]\n ],\n },\n \"hP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"],\n [\"K\", \"H_2\"]\n ],\n },\n \"hP2\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"K\": [\"1/3\", \"1/3\", \"0\"],\n \"H\": [\"1/3\", \"1/3\", \"1/2\"],\n \"H_2\": [\"1/3\", \"1/3\", \"-1/2\"],\n \"M\": [\"1/2\", \"0\", \"0\"],\n \"L\": [\"1/2\", \"0\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"M\"],\n [\"M\", \"K\"],\n [\"K\", \"GAMMA\"],\n [\"GAMMA\", \"A\"],\n [\"A\", \"L\"],\n [\"L\", \"H\"],\n [\"H\", \"A\"],\n [\"L\", \"M\"],\n [\"H\", \"K\"]\n ],\n },\n \"hR1\": {\n kparam: [\n [\"D\", \"aa/4/c/c\"],\n [\"Y\", \"5/6-2D\"],\n [\"N\", \"1/3+D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"L_2\": [\"0\", \"-1/2\", \"0\"],\n \"L_4\": [\"0\", \"0\", \"-1/2\"],\n \"F\": [\"1/2\", \"0\", \"1/2\"],\n \"F_2\": [\"1/2\", \"1/2\", \"0\"],\n \"S_0\": [\"N\", \"-N\", \"0\"],\n \"S_2\": [\"1-N\", \"0\", \"N\"],\n \"S_4\": [\"N\", \"0\", \"-N\"],\n \"S_6\": [\"1-N\", \"N\", \"0\"],\n \"H_0\": [\"1/2\", \"-1+Y\", \"1-Y\"],\n \"H_2\": [\"Y\", \"1-Y\", \"1/2\"],\n \"H_4\": [\"Y\", \"1/2\", \"1-Y\"],\n \"H_6\": [\"1/2\", \"1-Y\", \"-1+Y\"],\n \"M_0\": [\"N\", \"-1+Y\", \"N\"],\n \"M_2\": [\"1-N\", \"1-Y\", \"1-N\"],\n \"M_4\": [\"Y\", \"N\", \"N\"],\n \"M_6\": [\"1-N\", \"1-N\", \"1-Y\"],\n \"M_8\": [\"N\", \"N\", \"-1+Y\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"H_2\"],\n [\"H_0\", \"L\"],\n [\"L\", \"GAMMA\"],\n [\"GAMMA\", \"S_0\"],\n [\"S_2\", \"F\"],\n [\"F\", \"GAMMA\"]\n ],\n },\n \"hR2\": {\n kparam: [\n [\"Z\", \"1/6-cc/9/a/a\"],\n [\"H\", \"1/2-2Z\"],\n [\"N\", \"1/2+Z\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"P_0\": [\"H\", \"-1+H\", \"H\"],\n \"P_2\": [\"H\", \"H\", \"H\"],\n \"R_0\": [\"1-H\", \"-H\", \"-H\"],\n \"M\": [\"1-N\", \"-N\", \"1-N\"],\n \"M_2\": [\"N\", \"-1+N\", \"-1+N\"],\n \"L\": [\"1/2\", \"0\", \"0\"],\n \"F\": [\"1/2\", \"-1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"L\"],\n [\"L\", \"T\"],\n [\"T\", \"P_0\"],\n [\"P_2\", \"GAMMA\"],\n [\"GAMMA\", \"F\"]\n ],\n },\n \"mC1\": {\n kparam: [\n [\"Z\", \"(2+a/ccosbeta)/4/sinbeta/sinbeta\"],\n [\"H\", \"1/2-2Zccosbeta/a\"],\n [\"S\", \"3/4-bb/4/a/a/sinbeta/sinbeta\"],\n [\"P\", \"S-(3/4-S)acosbeta/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y_2\": [\"-1/2\", \"1/2\", \"0\"],\n \"Y_4\": [\"1/2\", \"-1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"C\": [\"1-S\", \"1-S\", \"0\"],\n \"C_2\": [\"-1+S\", \"S\", \"0\"],\n \"C_4\": [\"S\", \"-1+S\", \"0\"],\n \"D\": [\"-1+P\", \"P\", \"1/2\"],\n \"D_2\": [\"1-P\", \"1-P\", \"1/2\"],\n \"E\": [\"-1+Z\", \"1-Z\", \"1-H\"],\n \"E_2\": [\"-Z\", \"Z\", \"H\"],\n \"E_4\": [\"Z\", \"-Z\", \"1-H\"]\n },\n path: [\n [\"GAMMA\", \"C\"],\n [\"C_2\", \"Y_2\"],\n [\"Y_2\", \"GAMMA\"],\n [\"GAMMA\", \"M_2\"],\n [\"M_2\", \"D\"],\n [\"D_2\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC2\": {\n kparam: [\n [\"Z\", \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\"],\n [\"M\", \"(1+aa/b/b)/4\"],\n [\"D\", \"-accosbeta/2/b/b\"],\n [\"X\", \"1/2-2Zccosbeta/a\"],\n [\"P\", \"1+Z-2M\"],\n [\"S\", \"X-2D\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"1/2\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"F\": [\"-1+P\", \"1-P\", \"1-S\"],\n \"F_2\": [\"1-P\", \"P\", \"S\"],\n \"F_4\": [\"P\", \"1-P\", \"1-S\"],\n \"H\": [\"-Z\", \"Z\", \"X\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-X\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-X\"],\n \"G\": [\"-M\", \"M\", \"D\"],\n \"G_2\": [\"M\", \"1-M\", \"-D\"],\n \"G_4\": [\"M\", \"-M\", \"-D\"],\n \"G_6\": [\"1-M\", \"M\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"M\"],\n [\"M\", \"A\"],\n [\"A\", \"GAMMA\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mC3\": {\n kparam: [\n [\"Z\", \"(aa/b/b+(1+a/ccosbeta)/sinbeta/sinbeta)/4\"],\n [\"R\", \"1-Zbb/a/a\"],\n [\"E\", \"1/2-2Zccosbeta/a\"],\n [\"F\", \"E/2+aa/4/b/b+accosbeta/2/b/b\"],\n [\"U\", \"2F-Z\"],\n [\"W\", \"c/2/a/cosbeta(1-4U+aasinbetasinbeta/b/b)\"],\n [\"D\", \"-1/4+W/2-Zccosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"0\", \"0\", \"1/2\"],\n \"M_2\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"V\": [\"1/2\", \"0\", \"0\"],\n \"V_2\": [\"0\", \"1/2\", \"0\"],\n \"L_2\": [\"0\", \"1/2\", \"1/2\"],\n \"I\": [\"-1+R\", \"R\", \"1/2\"],\n \"I_2\": [\"1-R\", \"1-R\", \"1/2\"],\n \"K\": [\"-U\", \"U\", \"W\"],\n \"K_2\": [\"-1+U\", \"1-U\", \"1-W\"],\n \"K_4\": [\"1-U\", \"U\", \"W\"],\n \"H\": [\"-Z\", \"Z\", \"E\"],\n \"H_2\": [\"Z\", \"1-Z\", \"1-E\"],\n \"H_4\": [\"Z\", \"-Z\", \"1-E\"],\n \"N\": [\"-F\", \"F\", \"D\"],\n \"N_2\": [\"F\", \"1-F\", \"-D\"],\n \"N_4\": [\"F\", \"-F\", \"-D\"],\n \"N_6\": [\"1-F\", \"F\", \"D\"]\n },\n path: [\n [\"GAMMA\", \"A\"],\n [\"A\", \"I_2\"],\n [\"I\", \"M_2\"],\n [\"M_2\", \"GAMMA\"],\n [\"GAMMA\", \"Y\"],\n [\"L_2\", \"GAMMA\"],\n [\"GAMMA\", \"V_2\"]\n ],\n },\n \"mP1\": {\n kparam: [\n [\"Y\", \"(1+a/ccosbeta)/2/sinbeta/sinbeta\"],\n [\"N\", \"1/2+Yccosbeta/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"1/2\", \"0\"],\n \"B\": [\"0\", \"0\", \"1/2\"],\n \"B_2\": [\"0\", \"0\", \"-1/2\"],\n \"Y\": [\"1/2\", 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\"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oA2\": {\n kparam: [\n [\"X\", \"(1+cc/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC1\": {\n kparam: [\n [\"X\", \"(1+aa/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"-1/2\", \"1/2\", \"0\"],\n \"T\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"SIGMA_0\": [\"X\", \"X\", \"0\"],\n \"C_0\": [\"-X\", \"1-X\", \"0\"],\n \"A_0\": [\"X\", \"X\", \"1/2\"],\n \"E_0\": [\"-X\", \"1-X\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"A_0\"],\n [\"E_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oC2\": {\n kparam: [\n [\"X\", \"(1+bb/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Y\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"1/2\", \"1/2\", \"1/2\"],\n \"T_2\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"Z_2\": [\"0\", \"0\", \"-1/2\"],\n \"S\": [\"0\", \"1/2\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"R_2\": [\"0\", \"1/2\", \"-1/2\"],\n \"DELTA_0\": [\"-X\", \"X\", \"0\"],\n \"F_0\": [\"X\", \"1-X\", \"0\"],\n \"B_0\": [\"-X\", \"X\", \"1/2\"],\n \"B_2\": [\"-X\", \"X\", \"-1/2\"],\n \"G_0\": [\"X\", \"1-X\", \"1/2\"],\n \"G_2\": [\"X\", \"1-X\", \"-1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"F_0\"],\n [\"DELTA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"G_0\", \"T\"],\n [\"T\", \"Y\"],\n [\"GAMMA\", \"S\"],\n [\"S\", \"R\"],\n [\"R\", \"Z\"],\n [\"Z\", \"T\"]\n ],\n },\n \"oF1\": {\n kparam: [\n [\"J\", \"(1+aa/b/b-aa/c/c)/4\"],\n [\"H\", \"(1+aa/b/b+aa/c/c)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"1\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"SIGMA_0\": [\"0\", \"H\", \"H\"],\n \"U_0\": [\"1\", \"1-H\", \"1-H\"],\n \"A_0\": [\"1/2\", \"1/2+J\", \"J\"],\n \"C_0\": [\"1/2\", \"1/2-J\", \"1-J\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"GAMMA\"],\n [\"GAMMA\", \"SIGMA_0\"],\n [\"U_0\", \"T\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF2\": {\n kparam: [\n [\"J\", \"(1+cc/a/a-cc/b/b)/4\"],\n [\"K\", \"(1+cc/a/a+cc/b/b)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"1\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"LAMBDA_0\": [\"K\", \"K\", \"0\"],\n \"Q_0\": [\"1-K\", \"1-K\", \"1\"],\n \"G_0\": [\"1/2-J\", \"1-J\", \"1/2\"],\n \"H_0\": [\"1/2+J\", \"J\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"T\"],\n [\"T\", \"Z\"],\n [\"Z\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"Q_0\", \"Z\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oF3\": {\n kparam: [\n [\"H\", \"(1+aa/b/b-aa/c/c)/4\"],\n [\"K\", \"(1+bb/a/a-bb/c/c)/4\"],\n [\"P\", \"(1+cc/b/b-cc/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"Z\": [\"1/2\", \"1/2\", \"0\"],\n \"Y\": [\"1/2\", \"0\", \"1/2\"],\n \"A_0\": [\"1/2\", \"1/2+H\", \"H\"],\n \"C_0\": [\"1/2\", \"1/2-H\", \"1-H\"],\n \"B_0\": [\"1/2+K\", \"1/2\", \"K\"],\n \"D_0\": [\"1/2-K\", \"1/2\", \"1-K\"],\n \"G_0\": [\"P\", \"1/2+P\", \"1/2\"],\n \"H_0\": [\"1-P\", \"1/2-P\", \"1/2\"],\n \"L\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"Y\"],\n [\"Y\", \"C_0\"],\n [\"A_0\", \"Z\"],\n [\"Z\", \"B_0\"],\n [\"D_0\", \"T\"],\n [\"T\", \"G_0\"],\n [\"H_0\", \"Y\"],\n [\"T\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"GAMMA\", \"L\"]\n ],\n },\n \"oI1\": {\n kparam: [\n [\"Z\", \"(1+aa/c/c)/4\"],\n [\"H\", \"(1+bb/c/c)/4\"],\n [\"D\", \"(bb-aa)/4/c/c\"],\n [\"N\", \"(aa+bb)/4/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Z\", \"Z\", \"Z\"],\n \"F_2\": [\"Z\", \"1-Z\", \"-Z\"],\n \"Y_0\": [\"H\", \"-H\", \"H\"],\n \"U_0\": [\"1-H\", \"H\", \"-H\"],\n \"L_0\": [\"-N\", \"N\", \"1/2-D\"],\n \"M_0\": [\"N\", \"-N\", \"1/2+D\"],\n \"J_0\": [\"1/2-D\", \"1/2+D\", \"-N\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_2\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"Y_0\"],\n [\"U_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI2\": {\n kparam: [\n [\"Z\", \"(1+bb/a/a)/4\"],\n [\"H\", \"(1+cc/a/a)/4\"],\n [\"D\", \"(cc-bb)/4/a/a\"],\n [\"N\", \"(bb+cc)/4/a/a\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Y_0\": [\"Z\", \"-Z\", \"Z\"],\n \"U_2\": [\"-Z\", \"Z\", \"1-Z\"],\n \"LAMBDA_0\": [\"H\", \"H\", \"-H\"],\n \"G_2\": [\"-H\", \"1-H\", \"H\"],\n \"K\": [\"1/2-D\", \"-N\", \"N\"],\n \"K_2\": [\"1/2+D\", \"N\", \"-N\"],\n \"K_4\": [\"-N\", \"1/2-D\", \"1/2+D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"U_2\"],\n [\"Y_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_2\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oI3\": {\n kparam: [\n [\"Z\", \"(1+cc/b/b)/4\"],\n [\"Y\", \"(1+aa/b/b)/4\"],\n [\"D\", \"(aa-cc)/4/b/b\"],\n [\"M\", \"(cc+aa)/4/b/b\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"-1/2\", \"1/2\"],\n \"S\": [\"1/2\", \"0\", \"0\"],\n \"R\": [\"0\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"0\", \"1/2\"],\n \"W\": [\"1/4\", \"1/4\", \"1/4\"],\n \"SIGMA_0\": [\"-Y\", \"Y\", \"Y\"],\n \"F_0\": [\"Y\", \"-Y\", \"1-Y\"],\n \"LAMBDA_0\": [\"Z\", \"Z\", \"-Z\"],\n \"G_0\": [\"1-Z\", \"-Z\", \"Z\"],\n \"V_0\": [\"M\", \"1/2-D\", \"-M\"],\n \"H_0\": [\"-M\", \"1/2+D\", \"M\"],\n \"H_2\": [\"1/2+D\", \"-M\", \"1/2-D\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"F_0\"],\n [\"SIGMA_0\", \"GAMMA\"],\n [\"GAMMA\", \"LAMBDA_0\"],\n [\"G_0\", \"X\"],\n [\"GAMMA\", \"R\"],\n [\"R\", \"W\"],\n [\"W\", \"S\"],\n [\"S\", \"GAMMA\"],\n [\"GAMMA\", \"T\"],\n [\"T\", \"W\"]\n ],\n },\n \"oP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"X\": [\"1/2\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"U\": [\"1/2\", \"0\", \"1/2\"],\n \"Y\": [\"0\", \"1/2\", \"0\"],\n \"S\": [\"1/2\", \"1/2\", \"0\"],\n \"T\": [\"0\", \"1/2\", \"1/2\"],\n \"R\": [\"1/2\", \"1/2\", \"1/2\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"S\"],\n [\"S\", \"Y\"],\n [\"Y\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"U\"],\n [\"U\", \"R\"],\n [\"R\", \"T\"],\n [\"T\", \"Z\"],\n [\"X\", \"U\"],\n [\"Y\", \"T\"],\n [\"S\", \"R\"]\n ],\n },\n \"tI1\": {\n kparam: [\n [\"H\", \"(1+cc/a/a)/4\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"-1/2\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"Z\": [\"H\", \"H\", \"-H\"],\n \"Z_0\": [\"-H\", \"1-H\", \"H\"],\n \"N\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z_0\", \"M\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"]\n ],\n },\n \"tI2\": {\n kparam: [\n [\"H\", \"(1+aa/c/c)/4\"],\n [\"Z\", \"aa/2/c/c\"]\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"M\": [\"1/2\", \"1/2\", \"-1/2\"],\n \"X\": [\"0\", \"0\", \"1/2\"],\n \"P\": [\"1/4\", \"1/4\", \"1/4\"],\n \"N\": [\"0\", \"1/2\", \"0\"],\n \"S_0\": [\"-H\", \"H\", \"H\"],\n \"S\": [\"H\", \"1-H\", \"-H\"],\n \"R\": [\"-Z\", \"Z\", \"1/2\"],\n \"G\": [\"1/2\", \"1/2\", \"-Z\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"P\"],\n [\"P\", \"N\"],\n [\"N\", \"GAMMA\"],\n [\"GAMMA\", \"M\"],\n [\"M\", \"S\"],\n [\"S_0\", \"GAMMA\"],\n [\"X\", \"R\"],\n [\"G\", \"M\"]\n ],\n },\n \"tP1\": {\n kparam: [\n\n ],\n points: {\n \"GAMMA\": [\"0\", \"0\", \"0\"],\n \"Z\": [\"0\", \"0\", \"1/2\"],\n \"M\": [\"1/2\", \"1/2\", \"0\"],\n \"A\": [\"1/2\", \"1/2\", \"1/2\"],\n \"R\": [\"0\", \"1/2\", \"1/2\"],\n \"X\": [\"0\", \"1/2\", \"0\"]\n },\n path: [\n [\"GAMMA\", \"X\"],\n [\"X\", \"M\"],\n [\"M\", \"GAMMA\"],\n [\"GAMMA\", \"Z\"],\n [\"Z\", \"R\"],\n [\"R\", \"A\"],\n [\"A\", \"Z\"],\n [\"X\", \"R\"],\n [\"M\", \"A\"]\n ],\n },\n};\n\nexport const extBravaisLattices = Object.keys(bandPathData);\n","import type { MoyoDataset } from \"@spglib/moyo-wasm\";\nimport { Structure } from \"../../../structure\";\nimport { getSymmetry } from \"../spglib\";\nimport { spgroup_data } from \"../spgData\";\n\nimport { parameters } from \"../../../../lattice/parameters\";\n\nimport { determinant } from \"@/core/matrix/operations/determinant\";\nimport type { KPath } from \"@/core/kpoints\";\n\nimport { transformAP, determineExtBravais, determineAP } from \"./bravais\";\nimport {\n cellParams,\n evalExpr,\n evalExprSimple,\n extendKparam,\n getPmatrix,\n getPrimitive,\n getReciprocalCellRows,\n matrixFromRowMajor,\n vecMulMat,\n} from \"./seekpathTools\";\nimport { bandPathData } from \"./bandPathData\";\n\nconst RAD2DEG = 180 / Math.PI;\n\nfunction rowsFromFlat(data: ArrayLike<number>): number[][] {\n if (data.length !== 9) throw new Error(\"Expected 9 lattice values\");\n return [\n [data[0], data[1], data[2]],\n [data[3], data[4], data[5]],\n [data[6], data[7], data[8]],\n ];\n}\n\n/* Compute [a, b, c, alphaDeg, betaDeg, gammaDeg] from a row-major 3x3 lattice. /\nfunction cellParamsDegrees(data: ArrayLike<number>): number[] {\n const [a, b, c, cosalpha, cosbeta, cosgamma] = cellParams(\n matrixFromRowMajor(data),\n );\n const acos = (x: number) => Math.acos(Math.max(-1, Math.min(1, x))) RAD2DEG;\n return [a, b, c, acos(cosalpha), acos(cosbeta), acos(cosgamma)];\n}\n\n/** Determine the Seekpath extended Bravais lattice from symmetry data. /\nexport async function getSeekPathHighSymPath(\n structure: Structure,\n symTol = 1e-6,\n): Promise<string> {\n const symData = await getSymmetry(structure, symTol);\n\n const conventionalLattice = symData.conventional.lattice;\n const [a, b, c, alpha, beta, gamma] = parameters(conventionalLattice);\n const spgN = symData.calculationResults.number;\n\n const props = spgroup_data[spgN];\n if (!props) throw new Error(`No space group data for SG ${spgN}`);\n const bL = `${props[0]}${props[1]}`;\n\n if (bL === \"aP\") {\n return determineAP(conventionalLattice.basis);\n }\n\n return determineExtBravais(bL, spgN, a, b, c, alpha, beta, gamma);\n}\n\nexport interface GetPathOptions {\n withTimeReversal?: boolean;\n threshold?: number;\n symprec?: number;\n}\n\nexport interface SeekPathResult {\n readonly kpath: KPath;\n point_coords: Record<string, [number, number, number]>;\n path: [string, string][];\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n bravais_lattice: string;\n bravais_lattice_extended: string;\n conv_lattice: number[][];\n conv_positions: number[][];\n conv_types: number[];\n primitive_lattice: number[][];\n primitive_positions: number[][];\n primitive_types: number[];\n reciprocal_primitive_lattice: number[][];\n inverse_primitive_transformation_matrix: number[][];\n primitive_transformation_matrix: number[][];\n volume_original_wrt_conv: number;\n volume_original_wrt_prim: number;\n spacegroup_number: number;\n spacegroup_international: string;\n rotation_matrix: number[][];\n}\n\n/\n Return the k-point path information for a band structure, following the\n * HPKOT recipe. Mirrors `seekpath.get_path`.\n /\nexport async function getPath(\n structure: Structure,\n opts: GetPathOptions = {},\n): Promise<SeekPathResult> {\n const {\n withTimeReversal = true,\n threshold = 1e-7,\n symprec = 1e-5,\n } = opts;\n\n const symData = await getSymmetry(structure, symprec);\n const calcResults: MoyoDataset = symData.calculationResults;\n\n const stdCell = calcResults.std_cell;\n const convLatticeFlat = stdCell.lattice.basis;\n const convPositions = stdCell.positions.map((p) => Array.from(p));\n const convTypes = Array.from(stdCell.numbers);\n\n const spgrpNum = calcResults.number;\n const properties = spgroup_data[spgrpNum];\n if (!properties) {\n throw new Error(`No space group data for SG ${spgrpNum}`);\n }\n const bravaisLattice = `${properties[0]}${properties[1]}`;\n const hasInv = properties[2];\n\n const [a, b, c, alphaDeg, betaDeg, gammaDeg] = cellParamsDegrees(\n convLatticeFlat,\n );\n\n // Implement all different extended Bravais lattices\n let extBravais: string;\n let convLattice: number[][];\n let convPositionsFinal: number[][];\n\n if (bravaisLattice === \"aP\") {\n const ap = await transformAP(rowsFromFlat(convLatticeFlat), convPositions);\n extBravais = ap.extBravais;\n convLattice = ap.lattice;\n convPositionsFinal = ap.positions;\n } else {\n extBravais = determineExtBravais(\n bravaisLattice,\n spgrpNum,\n a,\n b,\n c,\n alphaDeg,\n betaDeg,\n gammaDeg,\n );\n convLattice = rowsFromFlat(convLatticeFlat);\n convPositionsFinal = convPositions;\n }\n\n // Primitive cell from the conventional cell via the HPKOT P matrix\n const primitive = getPrimitive(\n convLattice,\n convPositionsFinal,\n convTypes,\n bravaisLattice,\n );\n const { P, invP } = getPmatrix(bravaisLattice);\n\n // Get the path data (k-parameters definitions, point definitions, path)\n const data = bandPathData[extBravais];\n if (!data) throw new Error(`No band path data for extended Bravais ${extBravais}`);\n\n const [kparamDef, pointsDef, basePath] = [\n data.kparam,\n data.points,\n data.path,\n ];\n\n const cosalpha = Math.cos(alphaDeg Math.PI / 180);\n const cosbeta = Math.cos(betaDeg * Math.PI / 180);\n const cosgamma = Math.cos(gammaDeg * Math.PI / 180);\n\n const kparam: Record<string, number> = {};\n for (const [kparamName, kparamExpr] of kparamDef) {\n kparam[kparamName] = evalExpr(\n kparamExpr,\n a,\n b,\n c,\n cosalpha,\n cosbeta,\n cosgamma,\n kparam,\n );\n }\n const kparamExtended = extendKparam(kparam);\n\n const points: Record<string, [number, number, number]> = {};\n for (const [pointName, coordsDef] of Object.entries(pointsDef)) {\n points[pointName] = coordsDef.map((e) =>\n evalExprSimple(e, kparamExtended),\n ) as [number, number, number];\n }\n\n // If there is no inversion symmetry nor time-reversal symmetry, add\n // additional -k points\n const augmentedPath = !hasInv && !withTimeReversal;\n\n let path: [string, string][] = basePath;\n if (augmentedPath) {\n const negPoints: Record<string, [number, number, number]> = {};\n for (const [pointName, coords] of Object.entries(points)) {\n if (pointName === \"GAMMA\") continue;\n negPoints[`${pointName}'`] = [-coords[0], -coords[1], -coords[2]];\n }\n Object.assign(points, negPoints);\n\n const oldPath = basePath;\n const newSegments: [string, string][] = [];\n for (const [startP, endP] of oldPath) {\n newSegments.push([\n startP === \"GAMMA\" ? startP : `${startP}'`,\n endP === \"GAMMA\" ? endP : `${endP}'`,\n ]);\n }\n path = [...basePath, ...newSegments];\n }\n\n const primitiveMatrix = matrixFromRowMajor(primitive.lattice.flat());\n const reciprocalPrimitive = getReciprocalCellRows(primitiveMatrix);\n\n const origDet = Math.abs(\n determinant(matrixFromRowMajor(Array.from(structure.lattice.basis.data))),\n );\n const convDet = Math.abs(determinant(matrixFromRowMajor(convLattice.flat())));\n const primDet = Math.abs(determinant(primitiveMatrix));\n\n return {\n kpath: { kind: \"path\", points, segments: path },\n point_coords: points,\n path,\n has_inversion_symmetry: hasInv,\n augmented_path: augmentedPath,\n bravais_lattice: bravaisLattice,\n bravais_lattice_extended: extBravais,\n conv_lattice: convLattice,\n conv_positions: convPositionsFinal,\n conv_types: convTypes,\n primitive_lattice: primitive.lattice,\n primitive_positions: primitive.positions,\n primitive_types: primitive.types,\n reciprocal_primitive_lattice: Array.from(reciprocalPrimitive.data).reduce<\n number[][]\n >(\n (acc, x, i) => {\n acc[Math.floor(i / 3)][i % 3] = x;\n return acc;\n },\n [\n [0, 0, 0],\n [0, 0, 0],\n [0, 0, 0],\n ],\n ),\n inverse_primitive_transformation_matrix: invP,\n primitive_transformation_matrix: P,\n volume_original_wrt_conv: origDet / convDet,\n volume_original_wrt_prim: origDet / primDet,\n spacegroup_number: spgrpNum,\n spacegroup_international: calcResults.hm_symbol,\n rotation_matrix: rowsFromFlat(calcResults.std_rotation_matrix),\n };\n}\n\nexport interface ExplicitKPathResult extends SeekPathResult {\n explicit_kpoints_abs: number[][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_labels: string[];\n explicit_kpoints_linearcoord: number[];\n explicit_segments: [number, number][];\n}\n\nfunction vecAdd(a: readonly number[], b: readonly number[]): number[] {\n return [a[0] + b[0], a[1] + b[1], a[2] + b[2]];\n}\n\nfunction vecSub(a: readonly number[], b: readonly number[]): number[] {\n return [a[0] - b[0], a[1] - b[1], a[2] - b[2]];\n}\n\nfunction vecScale(a: readonly number[], k: number): number[] {\n return [a[0] * k, a[1] * k, a[2] * k];\n}\n\nfunction vecNorm(a: readonly number[]): number {\n return Math.hypot(a[0], a[1], a[2]);\n}\n\n/*\n Given the output of `getPath`, compute an \"explicit\" path, i.e. a full list\n * of k-points along each segment. Mirrors `seekpath.get_explicit_from_implicit`.\n /\nexport function getExplicitFromImplicit(\n result: Pick<SeekPathResult, \"kpath\" \| \"reciprocal_primitive_lattice\">,\n referenceDistance = 0.025,\n): {\n kpoints_rel: number[][];\n kpoints_abs: number[][];\n kpoints_labels: string[];\n kpoints_linearcoord: number[];\n segments: [number, number][];\n} {\n const recip = result.reciprocal_primitive_lattice;\n\n const kpointsRel: number[][] = [];\n const kpointsLabels: string[] = [];\n const kpointsLinearcoord: number[] = [];\n const segments: [number, number][] = [];\n let previousLinearcoord = 0;\n\n for (const [startLabel, stopLabel] of result.kpath.segments) {\n const startCoord = result.kpath.points[startLabel];\n const stopCoord = result.kpath.points[stopLabel];\n const startCoordAbs = vecMulMat(startCoord, recip);\n const stopCoordAbs = vecMulMat(stopCoord, recip);\n const segmentLength = vecNorm(vecSub(stopCoordAbs, startCoordAbs));\n const numPoints = Math.max(2, Math.floor(segmentLength / referenceDistance));\n\n let segmentStart = kpointsLabels.length;\n for (let i = 0; i < numPoints; i++) {\n // Skip the first point if it's the same as the last one of the\n // previous segment\n if (i === 0) {\n if (\n kpointsLabels.length &&\n kpointsLabels[kpointsLabels.length - 1] === startLabel\n ) {\n segmentStart -= 1;\n continue;\n }\n }\n\n kpointsRel.push(\n vecAdd(startCoord, vecScale(vecSub(stopCoord, startCoord), i / (numPoints - 1))),\n );\n if (i === 0) kpointsLabels.push(startLabel);\n else if (i === numPoints - 1) kpointsLabels.push(stopLabel);\n else kpointsLabels.push(\"\");\n kpointsLinearcoord.push(\n previousLinearcoord + (segmentLength i) / (numPoints - 1),\n );\n }\n previousLinearcoord += segmentLength;\n segments.push([segmentStart, kpointsLabels.length]);\n }\n\n return {\n kpoints_rel: kpointsRel,\n kpoints_abs: kpointsRel.map((p) => vecMulMat(p, recip)),\n kpoints_labels: kpointsLabels,\n kpoints_linearcoord: kpointsLinearcoord,\n segments,\n };\n}\n\n/*\n Return the k-point path for a band structure in scaled and absolute\n * coordinates, following the HPKOT recipe. Mirrors\n * `seekpath.get_explicit_k_path`.\n /\nexport async function getExplicitKPath(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<ExplicitKPathResult> {\n const { referenceDistance = 0.025, ...rest } = opts;\n const res = await getPath(structure, rest);\n const explicit = getExplicitFromImplicit(res, referenceDistance);\n\n return {\n ...res,\n explicit_kpoints_abs: explicit.kpoints_abs,\n explicit_kpoints_rel: explicit.kpoints_rel,\n explicit_kpoints_labels: explicit.kpoints_labels,\n explicit_kpoints_linearcoord: explicit.kpoints_linearcoord,\n explicit_segments: explicit.segments,\n };\n}\n\n// re-export for convenience\nexport { bandPathData } from \"./bandPathData\";\n","import { Structure } from \"../../../structure\";\n\nimport { getExplicitKPath } from \"./seekpath\";\nimport type { GetPathOptions } from \"./seekpath\";\nimport { getBZPolyhedron } from \"./bzPolyhedron\";\nimport { vecMulMat } from \"./seekpathTools\";\nimport type { KPath } from \"@/core/kpoints\";\n\n/* Data object compatible with the `brillouinzone-visualizer` widget. /\nexport interface BZVisualizerData {\n b1: number[];\n b2: number[];\n b3: number[];\n faces_data: {\n triangles_vertices: number[][];\n triangles: number[][];\n faces: number[][][];\n };\n kpoints: Record<string, number[]>;\n kpoints_rel: Record<string, number[]>;\n /* The high-symmetry path, serializable via `toKPOINTS`. /\n kpath: KPath;\n path: [string, string][];\n explicit_kpoints_rel: number[][];\n explicit_kpoints_linearcoord: number[];\n explicit_kpoints_labels: string[];\n explicit_kpoints_abs: number[][];\n explicit_segments: [number, number][];\n bravais_lattice: string;\n bravais_lattice_extended: string;\n spacegroup_number: number;\n spacegroup_international: string;\n has_inversion_symmetry: boolean;\n augmented_path: boolean;\n}\n\n/\n Run the HPKOT high-symmetry path computation and assemble the data object\n * consumed by the `brillouinzone-visualizer` web widget, mirroring the\n * seekpath example-data generator.\n /\nexport async function getBrillouinZoneData(\n structure: Structure,\n opts: GetPathOptions & { referenceDistance?: number } = {},\n): Promise<BZVisualizerData> {\n const res = await getExplicitKPath(structure, opts);\n\n const [b1, b2, b3] = res.reciprocal_primitive_lattice;\n const faces_data = getBZPolyhedron(b1, b2, b3);\n\n const kpoints: Record<string, number[]> = {};\n const kpoints_rel: Record<string, number[]> = {};\n for (const [label, rel] of Object.entries(res.kpath.points)) {\n kpoints_rel[label] = Array.from(rel);\n kpoints[label] = vecMulMat(rel, res.reciprocal_primitive_lattice);\n }\n\n return {\n b1,\n b2,\n b3,\n faces_data,\n kpoints,\n kpoints_rel,\n kpath: res.kpath,\n path: res.path,\n explicit_kpoints_rel: res.explicit_kpoints_rel,\n explicit_kpoints_linearcoord: res.explicit_kpoints_linearcoord,\n explicit_kpoints_labels: res.explicit_kpoints_labels,\n explicit_kpoints_abs: res.explicit_kpoints_abs,\n explicit_segments: res.explicit_segments,\n bravais_lattice: res.bravais_lattice,\n bravais_lattice_extended: res.bravais_lattice_extended,\n spacegroup_number: res.spacegroup_number,\n spacegroup_international: res.spacegroup_international,\n has_inversion_symmetry: res.has_inversion_symmetry,\n augmented_path: res.augmented_path,\n };\n}\n","/* Pauling electronegativity values keyed by element symbol. /\nexport const electronegativity: Record<string, number> = {\n Fr: 0.7,\n Cs: 0.79,\n Rb: 0.82,\n K: 0.82,\n Ba: 0.89,\n Ra: 0.9,\n Na: 0.93,\n Sr: 0.95,\n Li: 0.98,\n Ca: 1.0,\n Yb: 1.1,\n Eu: 1.2,\n Gd: 1.2,\n Tb: 1.1,\n La: 1.1,\n Ac: 1.1,\n Ce: 1.12,\n Pr: 1.13,\n Pm: 1.13,\n Am: 1.13,\n Nd: 1.14,\n Sm: 1.17,\n Dy: 1.22,\n Y: 1.22,\n Ho: 1.23,\n Er: 1.24,\n Tm: 1.25,\n Lu: 1.27,\n Cm: 1.28,\n Pu: 1.28,\n Np: 1.36,\n U: 1.38,\n Th: 1.3,\n Hf: 1.3,\n Zr: 1.33,\n Bk: 1.3,\n Cf: 1.3,\n Es: 1.3,\n Fm: 1.3,\n Md: 1.3,\n No: 1.3,\n Lr: 1.3,\n Pa: 1.5,\n Ta: 1.5,\n Ti: 1.54,\n Mn: 1.55,\n Mg: 1.31,\n Sc: 1.36,\n Be: 1.57,\n V: 1.63,\n Zn: 1.65,\n Cr: 1.66,\n Cd: 1.69,\n In: 1.78,\n Fe: 1.83,\n Co: 1.88,\n Ni: 1.91,\n Cu: 1.9,\n Ag: 1.93,\n Tl: 1.62,\n Nb: 1.6,\n Mo: 2.16,\n Tc: 1.9,\n Ru: 2.2,\n Rh: 2.28,\n Pd: 2.2,\n Sn: 1.96,\n Sb: 2.05,\n Te: 2.1,\n I: 2.66,\n Pt: 2.28,\n Au: 2.54,\n Hg: 2.0,\n Pb: 2.33,\n Bi: 2.02,\n Po: 2.0,\n At: 2.2,\n Ga: 1.81,\n Ge: 2.01,\n As: 2.18,\n Se: 2.55,\n Br: 2.96,\n Os: 2.2,\n Ir: 2.2,\n Re: 1.9,\n W: 2.36,\n Al: 1.61,\n Si: 1.9,\n P: 2.19,\n S: 2.58,\n Cl: 3.16,\n B: 2.04,\n C: 2.55,\n N: 3.04,\n O: 3.44,\n F: 3.98,\n H: 2.2,\n};\n","import { Structure } from \"../structure\";\nimport { gcd } from \"../../math/numeric\";\nimport { electronegativity } from \"../../data/periodictable/electronegativity\";\n\n/\n Count each element's occurrences in the structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to counts.\n /\nexport function composition(structure: Structure): Record<string, number> {\n const out: Record<string, number> = {};\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n out[symbol] ??= 0;\n out[symbol]++;\n }\n\n return out;\n}\n\nfunction compositionGCD(comp: Record<string, number>): number {\n const values = Object.values(comp);\n\n return values.reduce((a, b) => gcd(a, b));\n}\n\nfunction hillOrder(elements: string[]): string[] {\n if (!elements.includes(\"C\")) {\n return [...elements].sort();\n }\n\n const rest = elements.filter((e) => e !== \"C\" && e !== \"H\").sort();\n\n return [\"C\", ...(elements.includes(\"H\") ? [\"H\"] : []), ...rest];\n}\n\nfunction alphabeticalOrder(elements: string[]): string[] {\n return [...elements].sort();\n}\n\nfunction iupacOrder(elements: string[]): string[] {\n return [...elements].sort((a, b) => {\n const ea = electronegativity[a];\n const eb = electronegativity[b];\n\n if (ea === undefined && eb === undefined) return a.localeCompare(b);\n if (ea === undefined) return 1;\n if (eb === undefined) return -1;\n\n return ea - eb \|\| a.localeCompare(b);\n });\n}\n\nfunction formulaFromComposition(\n comp: Record<string, number>,\n ordering: (elements: string[]) => string[],\n): string {\n const elements = ordering(Object.keys(comp));\n\n return elements\n .map((el) => {\n const count = comp[el];\n\n return count === 1 ? el : `${el}${count}`;\n })\n .join(\"\");\n}\n\nexport function reducedComposition(\n comp: Record<string, number>,\n): Record<string, number> {\n const factor = compositionGCD(comp);\n\n const out: Record<string, number> = {};\n\n for (const [element, count] of Object.entries(comp)) {\n out[element] = count / factor;\n }\n\n return out;\n}\n\nconst SUBSCRIPT_DIGITS = [\"₀\", \"₁\", \"₂\", \"₃\", \"₄\", \"₅\", \"₆\", \"₇\", \"₈\", \"₉\"];\n\nconst SUBSCRIPT_TO_DIGIT: Record<string, string> = {\n \"₀\": \"0\",\n \"₁\": \"1\",\n \"₂\": \"2\",\n \"₃\": \"3\",\n \"₄\": \"4\",\n \"₅\": \"5\",\n \"₆\": \"6\",\n \"₇\": \"7\",\n \"₈\": \"8\",\n \"₉\": \"9\",\n};\n\n/* Label for anonymous formula ordering: 0 -> A, 25 -> Z, 26 -> AA, ... /\nfunction anonymousLabel(index: number): string {\n let out = \"\";\n let n = index;\n\n do {\n out = String.fromCharCode(65 + (n % 26)) + out;\n n = Math.floor(n / 26) - 1;\n } while (n >= 0);\n\n return out;\n}\n\nfunction formulaWithSubscripts(formula: string): string {\n return formula.replace(/\\d+/g, (digits) =>\n Array.from(digits, (d) => SUBSCRIPT_DIGITS[Number(d)]).join(\"\"),\n );\n}\n\nfunction anonymousFromComposition(comp: Record<string, number>): string {\n const entries = Object.entries(comp).sort(\n (a, b) => b[1] - a[1] \|\| a[0].localeCompare(b[0]),\n );\n\n return entries\n .map(([, count], i) => {\n const label = anonymousLabel(i);\n\n return count === 1 ? label : `${label}${count}`;\n })\n .join(\"\");\n}\n\nfunction mergeInto(\n target: Record<string, number>,\n source: Record<string, number>,\n multiplier: number,\n): void {\n for (const [element, count] of Object.entries(source)) {\n target[element] = (target[element] ?? 0) + count multiplier;\n }\n}\n\nfunction tokenizeFormula(text: string): string[] {\n const tokens: string[] = [];\n let i = 0;\n\n while (i < text.length) {\n const ch = text[i];\n\n if (/\\s/.test(ch)) {\n i++;\n } else if (\"()[]{}\".includes(ch)) {\n tokens.push(ch);\n i++;\n } else if (/[A-Z]/.test(ch)) {\n let j = i + 1;\n while (j < text.length && /[a-z]/.test(text[j])) j++;\n tokens.push(text.slice(i, j));\n i = j;\n } else if (/[0-9]/.test(ch)) {\n let j = i;\n while (j < text.length && /[0-9]/.test(text[j])) j++;\n\n if (text[j] === \".\" && /[0-9]/.test(text[j + 1] ?? \"\")) {\n j++;\n while (j < text.length && /[0-9]/.test(text[j])) j++;\n }\n\n tokens.push(text.slice(i, j));\n i = j;\n } else {\n throw new Error(`Invalid character '${ch}' in formula`);\n }\n }\n\n return tokens;\n}\n\nfunction assertBalanced(text: string): void {\n const pairs: Record<string, string> = { \"(\": \")\", \"[\": \"]\", \"{\": \"}\" };\n const stack: string[] = [];\n\n for (const ch of text) {\n if (ch === \"(\" \|\| ch === \"[\" \|\| ch === \"{\") {\n stack.push(ch);\n } else if (ch === \")\" \|\| ch === \"]\" \|\| ch === \"}\") {\n const top = stack.pop();\n\n if (top === undefined \|\| pairs[top] !== ch) {\n throw new Error(`Unbalanced brackets in formula: ${text}`);\n }\n }\n }\n\n if (stack.length > 0) {\n throw new Error(`Unbalanced brackets in formula: ${text}`);\n }\n}\n\nfunction parseTokens(tokens: string[]): Record<string, number> {\n let idx = 0;\n const isNumber = (tok: string): boolean => /^[0-9]/.test(tok);\n\n function readCount(): number {\n const tok = tokens[idx];\n\n if (tok !== undefined && isNumber(tok)) {\n idx++;\n return Number(tok);\n }\n\n return 1;\n }\n\n function parseGroup(): Record<string, number> {\n const comp: Record<string, number> = {};\n let leading = 1;\n\n if (idx < tokens.length && isNumber(tokens[idx])) {\n leading = Number(tokens[idx]);\n idx++;\n }\n\n while (idx < tokens.length) {\n const tok = tokens[idx];\n\n if (tok === \")\" \|\| tok === \"]\" \|\| tok === \"}\") break;\n\n if (tok === \"(\" \|\| tok === \"[\" \|\| tok === \"{\") {\n idx++;\n const inner = parseGroup();\n idx++;\n mergeInto(comp, inner, readCount());\n continue;\n }\n\n if (isNumber(tok)) {\n throw new Error(`Unexpected number '${tok}' in formula`);\n }\n\n const symbol = tok;\n idx++;\n comp[symbol] = (comp[symbol] ?? 0) + readCount();\n }\n\n if (leading !== 1) {\n for (const element of Object.keys(comp)) {\n comp[element] = leading;\n }\n }\n\n return comp;\n }\n\n const result: Record<string, number> = {};\n\n while (idx < tokens.length) {\n mergeInto(result, parseGroup(), 1);\n\n if (idx < tokens.length) {\n throw new Error(\"Unbalanced brackets in formula\");\n }\n }\n\n return result;\n}\n\n/\n Return the Hill-ordered chemical formula of a structure.\n * @param structure - Structure to evaluate.\n * @returns Hill-formula string.\n /\nexport function hillFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), hillOrder);\n}\n\n/\n Return the reduced Hill-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced formula string.\n /\nexport function reducedFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n );\n}\n\n/\n Return the alphabetically-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Alphabetical-formula string.\n /\nexport function alphabeticalFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), alphabeticalOrder);\n}\n\n/\n Return the reduced alphabetically-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced alphabetical-formula string.\n /\nexport function reducedAlphabeticalFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n alphabeticalOrder,\n );\n}\n\n/\n Return the IUPAC-ordered chemical formula (by increasing electronegativity).\n * @param structure - Structure to evaluate.\n * @returns IUPAC-formula string.\n /\nexport function iupacFormula(structure: Structure): string {\n return formulaFromComposition(composition(structure), iupacOrder);\n}\n\n/\n Return the reduced IUPAC-ordered chemical formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced IUPAC-formula string.\n /\nexport function reducedIUPACFormula(structure: Structure): string {\n return formulaFromComposition(\n reducedComposition(composition(structure)),\n iupacOrder,\n );\n}\n\n/\n Return an anonymous formula where elements are labeled A, B, C, ...\n * by decreasing abundance.\n * @param structure - Structure to evaluate.\n * @returns Anonymous-formula string.\n /\nexport function anonymousFormula(structure: Structure): string {\n return anonymousFromComposition(composition(structure));\n}\n\n/\n Return the reduced anonymous formula.\n * @param structure - Structure to evaluate.\n * @returns Reduced anonymous-formula string.\n /\nexport function reducedAnonymousFormula(structure: Structure): string {\n return anonymousFromComposition(reducedComposition(composition(structure)));\n}\n\n/\n Return the Hill-ordered formula with Unicode subscript digits.\n * @param structure - Structure to evaluate.\n * @returns Formula string with subscript digits.\n /\nexport function subscriptFormula(structure: Structure): string {\n return formulaWithSubscripts(\n formulaFromComposition(composition(structure), hillOrder),\n );\n}\n\n/\n Return the reduced Hill-ordered formula with Unicode subscript digits.\n * @param structure - Structure to evaluate.\n * @returns Reduced formula string with subscript digits.\n /\nexport function reducedSubscriptFormula(structure: Structure): string {\n return formulaWithSubscripts(\n formulaFromComposition(\n reducedComposition(composition(structure)),\n hillOrder,\n ),\n );\n}\n\n/\n Parse a chemical formula string into a composition.\n \n Supports element symbols, integer and decimal counts, nested bracket\n * groups (e.g. \"(NH4)2SO4\"), and dot/asterisk separated hydrate segments\n * (e.g. \"CaSO4·2H2O\" or \"CaSO42H2O\").\n @param text - Formula string to parse.\n * @returns Map of element symbols to counts.\n /\nexport function parseFormula(text: string): Record<string, number> {\n if (text.trim().length === 0) {\n throw new Error(\"Formula string is empty\");\n }\n\n const normalized = text.replace(/[₀-₉]/g, (ch) => SUBSCRIPT_TO_DIGIT[ch]);\n assertBalanced(normalized);\n\n const result: Record<string, number> = {};\n\n for (const segment of normalized.split(/[·]/)) {\n if (segment.length === 0) continue;\n\n mergeInto(result, parseTokens(tokenizeFormula(segment)), 1);\n }\n\n return result;\n}\n\n/*\n Count the total number of atoms (sites) in the structure.\n * @param structure - Structure to evaluate.\n * @returns Number of atoms.\n /\nexport function numAtoms(structure: Structure): number {\n return structure.sites.length;\n}\n","import type { Structure } from \"../../structure/structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nexport interface AssignmentResult {\n /* For each site i in A, the matched site index in B (or -1 if unassigned). /\n assignment: Int32Array;\n /* Per-site distances in the same order as A's sites. /\n distances: Float64Array;\n rms: number;\n maxDistance: number;\n}\n\n/* O(n^3) Hungarian (Kuhn–Munkres) solver for a square cost matrix.\n * Returns the column index assigned to each row. /\nfunction hungarian(cost: number[][]): number[] {\n const n = cost.length;\n const INF = Number.POSITIVE_INFINITY;\n\n const u = new Array<number>(n + 1).fill(0);\n const v = new Array<number>(n + 1).fill(0);\n const p = new Array<number>(n + 1).fill(0);\n const way = new Array<number>(n + 1).fill(0);\n\n for (let i = 1; i <= n; i++) {\n p[0] = i;\n let j0 = 0;\n const minv = new Array<number>(n + 1).fill(INF);\n const used = new Array<boolean>(n + 1).fill(false);\n\n do {\n used[j0] = true;\n const i0 = p[j0];\n let delta = INF;\n let j1 = -1;\n\n for (let j = 1; j <= n; j++) {\n if (!used[j]) {\n const cur = cost[i0 - 1][j - 1] - u[i0] - v[j];\n if (cur < minv[j]) {\n minv[j] = cur;\n way[j] = j0;\n }\n if (minv[j] < delta) {\n delta = minv[j];\n j1 = j;\n }\n }\n }\n\n for (let j = 0; j <= n; j++) {\n if (used[j]) {\n u[p[j]] += delta;\n v[j] -= delta;\n } else {\n minv[j] -= delta;\n }\n }\n\n j0 = j1;\n } while (p[j0] !== 0);\n\n do {\n const j1 = way[j0];\n p[j0] = p[j1];\n j0 = j1;\n } while (j0);\n }\n\n const result = new Array<number>(n);\n for (let j = 1; j <= n; j++) {\n result[p[j] - 1] = j - 1;\n }\n return result;\n}\n\n/* Group site indices by species symbol. /\nfunction groupBySpecies(structure: Structure): Map<string, number[]> {\n const groups = new Map<string, number[]>();\n structure.sites.forEach((site, index) => {\n const symbol = site.species.symbol;\n let list = groups.get(symbol);\n if (!list) {\n list = [];\n groups.set(symbol, list);\n }\n list.push(index);\n });\n return groups;\n}\n\n/\n Squared minimum-image distance between two fractional coordinates in the\n * lattice described by the metric tensor `G` (row-major 3x3). For non-orthogonal\n * lattices the true nearest image is found by searching small integer shifts.\n /\nfunction squaredMinimumImageDistance(\n fa: Float64Array,\n fb: Float64Array,\n G: Float64Array,\n): number {\n const dx = fb[0] - fa[0];\n const dy = fb[1] - fa[1];\n const dz = fb[2] - fa[2];\n\n let best = Number.POSITIVE_INFINITY;\n\n for (let i = -1; i <= 1; i++) {\n const x = dx - i;\n for (let j = -1; j <= 1; j++) {\n const y = dy - j;\n for (let k = -1; k <= 1; k++) {\n const z = dz - k;\n const d =\n x (G[0] * x + G[1] * y + G[2] * z) +\n y * (G[3] * x + G[4] * y + G[5] * z) +\n z * (G[6] * x + G[7] * y + G[8] * z);\n if (d < best) best = d;\n }\n }\n }\n\n return best < 0 ? 0 : best;\n}\n\n/*\n Find the optimal (minimum sum-of-squared distance) assignment of the sites of\n * `structureA` onto those of `structureB`, constrained so that matched sites\n * share the same species.\n \n Distances use the minimum-image convention in `structureA`'s metric, which\n * implicitly accounts for any lattice translation.\n \n Returns `null` when no species-valid complete assignment exists (i.e. the two\n * structures do not contain the same multiset of species).\n /\nexport function assignSites(\n structureA: Structure,\n structureB: Structure,\n maxPairDistance?: number,\n): AssignmentResult \| null {\n const groupsA = groupBySpecies(structureA);\n const groupsB = groupBySpecies(structureB);\n\n for (const [symbol, indicesA] of groupsA) {\n const indicesB = groupsB.get(symbol);\n if (!indicesB \|\| indicesB.length !== indicesA.length) {\n return null;\n }\n }\n\n const n = structureA.sites.length;\n const assignment = new Int32Array(n).fill(-1);\n const distances = new Float64Array(n);\n const G = metricTensor(structureA.lattice).data;\n\n const fracA = structureA.sites.map((site) => site.frac);\n const fracB = structureB.sites.map((site) => site.frac);\n\n const capSq =\n maxPairDistance !== undefined ? maxPairDistance maxPairDistance : Number.POSITIVE_INFINITY;\n\n let sumSquared = 0;\n let maxDist = 0;\n\n for (const [symbol, indicesA] of groupsA) {\n const indicesB = groupsB.get(symbol)!;\n const m = indicesA.length;\n\n if (m === 0) continue;\n\n const cost: number[][] = Array.from({ length: m }, () =>\n new Array<number>(m).fill(0),\n );\n\n for (let i = 0; i < m; i++) {\n const a = fracA[indicesA[i]];\n for (let j = 0; j < m; j++) {\n const b = fracB[indicesB[j]];\n const d = squaredMinimumImageDistance(a, b, G);\n cost[i][j] =\n capSq !== Number.POSITIVE_INFINITY && d > capSq\n ? Number.POSITIVE_INFINITY\n : d;\n }\n }\n\n // If any site has no partner within tolerance, no assignment within\n // tolerance is possible — skip the O(n³) Hungarian solver entirely.\n for (let i = 0; i < m; i++) {\n let feasible = false;\n for (let j = 0; j < m; j++) {\n if (cost[i][j] !== Number.POSITIVE_INFINITY) {\n feasible = true;\n break;\n }\n }\n if (!feasible) return null;\n }\n for (let j = 0; j < m; j++) {\n let feasible = false;\n for (let i = 0; i < m; i++) {\n if (cost[i][j] !== Number.POSITIVE_INFINITY) {\n feasible = true;\n break;\n }\n }\n if (!feasible) return null;\n }\n\n // Replace any remaining infinities with a huge finite cost so the solver\n // (which assumes finite costs) completes safely for the rare infeasible\n // case not caught above (a Hall violation). Such a match is rejected by the\n // rms check downstream.\n const BIG = 1e18;\n for (let i = 0; i < m; i++) {\n for (let j = 0; j < m; j++) {\n if (cost[i][j] === Number.POSITIVE_INFINITY) cost[i][j] = BIG;\n }\n }\n\n const perm = hungarian(cost);\n\n for (let i = 0; i < m; i++) {\n const aIndex = indicesA[i];\n const bIndex = indicesB[perm[i]];\n const distance = Math.sqrt(cost[i][perm[i]]);\n assignment[aIndex] = bIndex;\n distances[aIndex] = distance;\n sumSquared += distance * distance;\n if (distance > maxDist) maxDist = distance;\n }\n }\n\n const rms = n > 0 ? Math.sqrt(sumSquared / n) : 0;\n\n return { assignment, distances, rms, maxDistance: maxDist };\n}\n","import { Structure } from \"../../structure/structure\";\nimport { composition } from \"../../properties/formula\";\nimport { gcd } from \"../../../math/numeric\";\nimport { canonicalize } from \"../canonicalize\";\nimport { getSymmetry } from \"./spglib\";\nimport { assignSites } from \"./assign\";\nimport { applyTransformationBasis } from \"../applyTransformationBasis\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\nimport { createMatrix } from \"@/core/matrix/matrix\";\nimport type { Matrix } from \"@/core/matrix/matrix\";\n\nexport interface StructureMatchResult {\n matches: boolean;\n rms: number \| null;\n maxDistance: number \| null;\n distances: Float64Array \| null;\n}\n\ninterface SiteMatch {\n rms: number;\n maxDistance: number;\n distances: Float64Array;\n}\n\nfunction reducedComposition(\n comp: Record<string, number>,\n): Record<string, number> {\n const counts = Object.values(comp);\n\n if (counts.length === 0) {\n return {};\n }\n\n const factor = counts.reduce((a, b) => gcd(a, b));\n const reduced: Record<string, number> = {};\n\n for (const [element, count] of Object.entries(comp)) {\n reduced[element] = count / factor;\n }\n\n return reduced;\n}\n\nfunction sameComposition(\n compA: Record<string, number>,\n compB: Record<string, number>,\n): boolean {\n const elementsA = Object.keys(compA).sort();\n const elementsB = Object.keys(compB).sort();\n\n if (elementsA.length !== elementsB.length) {\n return false;\n }\n\n return elementsA.every(\n (element, index) =>\n element === elementsB[index] && compA[element] === compB[element],\n );\n}\n\nfunction noMatch(): StructureMatchResult {\n return {\n matches: false,\n rms: null,\n maxDistance: null,\n distances: null,\n };\n}\n\nfunction wrapComponent(x: number): number {\n const v = x - Math.floor(x);\n return Math.abs(v) < 1e-12 ? 0 : v;\n}\n\n/** Apply a symmetry operation (rotation + translation, in fractional lattice\n * coordinates) to a structure's sites, keeping its lattice unchanged. /\nfunction applySymmetryOperation(\n structure: Structure,\n rotation: number[],\n translation: number[],\n): Structure {\n const sites = structure.sites.map((site) => {\n const f = site.frac;\n const x =\n rotation[0] f[0] +\n rotation[1] * f[1] +\n rotation[2] * f[2] +\n translation[0];\n const y =\n rotation[3] * f[0] +\n rotation[4] * f[1] +\n rotation[5] * f[2] +\n translation[1];\n const z =\n rotation[6] * f[0] +\n rotation[7] * f[1] +\n rotation[8] * f[2] +\n translation[2];\n\n return {\n ...site,\n frac: new Float64Array([\n wrapComponent(x),\n wrapComponent(y),\n wrapComponent(z),\n ]),\n };\n });\n\n return { ...structure, sites };\n}\n\n/** Apply a constant fractional translation to a structure's sites. /\nfunction translateStructure(\n structure: Structure,\n translation: number[],\n): Structure {\n return {\n ...structure,\n sites: structure.sites.map((site) => {\n const f = site.frac;\n return {\n ...site,\n frac: new Float64Array([\n wrapComponent(f[0] + translation[0]),\n wrapComponent(f[1] + translation[1]),\n wrapComponent(f[2] + translation[2]),\n ]),\n };\n }),\n };\n}\n\n/\n Distinct global translations that could align `candidate` onto `a`.\n \n Anchors a site belonging to the least-common shared species in `a` and\n * aligns it to every same-species site in `candidate`. The true alignment is\n * always recovered by one of these translations, while choosing the rarest\n * shared species minimizes the number of candidates that must be tested.\n /\nfunction candidateTranslations(a: Structure, candidate: Structure): number[][] {\n const candidateSpecies = new Set(\n candidate.sites.map((site) => site.species.symbol),\n );\n\n // Pick the shared species with the fewest sites in `a`.\n const counts = new Map<string, number>();\n\n for (const site of a.sites) {\n const symbol = site.species.symbol;\n\n if (candidateSpecies.has(symbol)) {\n counts.set(symbol, (counts.get(symbol) ?? 0) + 1);\n }\n }\n\n let anchorSpecies = \"\";\n let anchorCount = Infinity;\n\n for (const [symbol, count] of counts) {\n if (count < anchorCount) {\n anchorSpecies = symbol;\n anchorCount = count;\n }\n }\n\n if (!anchorSpecies) return [];\n\n const anchorIndex = a.sites.findIndex(\n (site) => site.species.symbol === anchorSpecies,\n );\n\n if (anchorIndex < 0) return [];\n\n const fa = a.sites[anchorIndex].frac;\n const seen = new Set<string>();\n const out: number[][] = [];\n\n for (const site of candidate.sites) {\n if (site.species.symbol !== anchorSpecies) continue;\n\n const fb = site.frac;\n\n const t = [\n wrapComponent(fa[0] - fb[0]),\n wrapComponent(fa[1] - fb[1]),\n wrapComponent(fa[2] - fb[2]),\n ];\n\n const key = `${t[0].toFixed(4)},${t[1].toFixed(4)},${t[2].toFixed(4)}`;\n\n if (!seen.has(key)) {\n seen.add(key);\n out.push(t);\n }\n }\n\n return out;\n}\n\n/* The 6 lattice-vector permutation matrices (row permutations). /\nfunction latticePermutations(): Matrix[] {\n const perms: number[][] = [\n [0, 1, 2],\n [0, 2, 1],\n [1, 0, 2],\n [1, 2, 0],\n [2, 0, 1],\n [2, 1, 0],\n ];\n\n return perms.map((perm) => {\n const data = new Float64Array(9);\n for (let r = 0; r < 3; r++) {\n data[r 3 + perm[r]] = 1;\n }\n return createMatrix(3, 3, data);\n });\n}\n\n/*\n All integer rotation matrices (entries in {-1, 0, 1}, determinant ±1) that\n * preserve the lattice metric `G`. This is the full lattice point group — a\n * superset of the space-group rotations returned by symmetry analysis and\n * robust to the basis/origin choices made by cell standardization.\n /\nfunction latticePointGroup(G: Float64Array): number[][] {\n const values = [-1, 0, 1];\n const out: number[][] = [];\n\n for (let idx = 0; idx < 19683; idx++) {\n const M = new Array<number>(9);\n let x = idx;\n for (let k = 0; k < 9; k++) {\n M[k] = values[x % 3];\n x = Math.floor(x / 3);\n }\n\n const det =\n M[0] (M[4] * M[8] - M[5] * M[7]) -\n M[1] * (M[3] * M[8] - M[5] * M[6]) +\n M[2] * (M[3] * M[7] - M[4] * M[6]);\n\n if (det !== 1 && det !== -1) continue;\n\n let preserves = true;\n for (let r = 0; r < 3 && preserves; r++) {\n for (let c = 0; c < 3; c++) {\n let s = 0;\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n s += M[r * 3 + i] * G[i * 3 + j] * M[c * 3 + j];\n }\n }\n if (Math.abs(s - G[r * 3 + c]) > 1e-6) {\n preserves = false;\n break;\n }\n }\n }\n\n if (preserves) out.push(M);\n }\n\n return out;\n}\n\n/*\n Match two structures using symmetry-normalized primitive cells, mirroring the\n * behaviour of pymatgen's `StructureMatcher` (primitive-cell matching with\n * symmetry-operation search and RMS tolerance).\n /\nexport async function matchStructures(\n structureA: Structure,\n structureB: Structure,\n tolerance = 0.3,\n symprec = 1e-4,\n): Promise<StructureMatchResult> {\n const reducedA = reducedComposition(composition(structureA));\n const reducedB = reducedComposition(composition(structureB));\n\n if (!sameComposition(reducedA, reducedB)) {\n return noMatch();\n }\n\n const [symmetryA, symmetryB] = await Promise.all([\n getSymmetry(structureA, symprec),\n getSymmetry(structureB, symprec),\n ]);\n\n const a = canonicalize(symmetryA.primitive);\n const b = canonicalize(symmetryB.primitive);\n\n if (a.sites.length !== b.sites.length) {\n return noMatch();\n }\n\n if (a.sites.length === 0) {\n return {\n matches: true,\n rms: 0,\n maxDistance: 0,\n distances: new Float64Array(),\n };\n }\n\n // Candidate rotations: the full lattice point group of `a` (rotations that\n // preserve its metric). This covers all symmetry-equivalent placements of `b`\n // within `a`'s frame, regardless of the basis/origin choice made during\n // standardization.\n const G = metricTensor(a.lattice).data;\n const rotations = latticePointGroup(G);\n const permutations = latticePermutations();\n\n let best: SiteMatch \| null = null;\n\n const consider = (candidate: Structure) => {\n const result = assignSites(a, candidate, tolerance);\n if (result === null) return;\n if (best === null \|\| result.rms < best.rms) {\n best = {\n rms: result.rms,\n maxDistance: result.maxDistance,\n distances: result.distances,\n };\n }\n };\n\n const evaluate = (candidate: Structure): boolean => {\n // Direct placement (no extra translation) — resolves well-behaved cases.\n consider(candidate);\n if (best !== null && best.rms <= tolerance) return true;\n\n // Search the global translation that aligns the two (handles origin-choice\n // differences between standardized primitives).\n for (const t of candidateTranslations(a, candidate)) {\n consider(translateStructure(candidate, t));\n if (best !== null && best.rms <= tolerance) return true;\n }\n\n return false;\n };\n\n // Iterate over lattice-vector relabellings of `b` (covers basis-ordering\n // choices) combined with every lattice point-group rotation.\n for (let p = 0; p < permutations.length; p++) {\n const bPerm = p === 0 ? b : applyTransformationBasis(b, permutations[p]);\n\n for (const rotation of rotations) {\n if (evaluate(applySymmetryOperation(bPerm, rotation, [0, 0, 0]))) {\n return {\n matches: true,\n rms: best!.rms,\n maxDistance: best!.maxDistance,\n distances: best!.distances,\n };\n }\n }\n }\n\n if (best === null) {\n return noMatch();\n }\n\n return {\n matches: best.rms <= tolerance,\n rms: best.rms,\n maxDistance: best.maxDistance,\n distances: best.distances,\n };\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Minimum-image distance between two sites. /\nexport function getDistance(\n structure: Structure,\n idx1: number,\n idx2: number,\n): number {\n const displacement = getDisplacement(structure, idx1, idx2);\n\n const G = metricTensor(structure.lattice).data;\n\n return Math.sqrt(distanceSquared(displacement, G));\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Distances from site `idx` to every other site. /\nexport function getDistances(structure: Structure, idx: number): Float64Array {\n const n = structure.sites.length;\n const out = new Float64Array(n);\n\n const G = metricTensor(structure.lattice).data;\n\n for (let j = 0; j < n; j++) {\n if (j === idx) {\n out[j] = 0;\n continue;\n }\n\n const disp = getDisplacement(structure, idx, j);\n\n out[j] = Math.sqrt(distanceSquared(disp, G));\n }\n\n return out;\n}\n","import { Structure } from \"../../structure\";\nimport { metricTensor } from \"../../../lattice/metricTensor\";\n\nimport { distanceSquared } from \"./utils\";\nimport { getDisplacement } from \"./getDisplacement\";\n\n/* Pairwise distance matrix for all sites, stored as an array of Float64Array rows. /\nexport function getDistancesMatrix(structure: Structure): Float64Array[] {\n const n = structure.sites.length;\n\n const matrix: Float64Array[] = Array.from(\n { length: n },\n () => new Float64Array(n),\n );\n\n const G = metricTensor(structure.lattice).data;\n\n for (let i = 0; i < n; i++) {\n matrix[i][i] = 0;\n\n for (let j = i + 1; j < n; j++) {\n const disp = getDisplacement(structure, i, j);\n\n const d = Math.sqrt(distanceSquared(disp, G));\n\n matrix[i][j] = d;\n matrix[j][i] = d;\n }\n }\n\n return matrix;\n}\n","import { Structure } from \"../../structure\";\nimport { Site } from \"../../../site/site\";\n\n// generic method for finding sites on a given condition.\n\n/* Find site indices matching a predicate. /\nexport function findSites(\n structure: Structure,\n predicate: (site: Site, index: number) => boolean,\n): number[] {\n const indices: number[] = [];\n\n for (let i = 0; i < structure.sites.length; i++) {\n if (predicate(structure.sites[i], i)) {\n indices.push(i);\n }\n }\n\n return indices;\n}\n","import { Species } from \"../../../species/species\";\nimport { Structure } from \"../../structure\";\nimport { findSites } from \"./findSites\";\n\n// matches species.symbol only.\n\n/* Find site indices whose species symbol matches the given species or string. /\nexport function findSitesBySpecies(\n structure: Structure,\n species: Species \| string,\n): number[] {\n const symbol = typeof species === \"string\" ? species : species.symbol;\n\n return findSites(structure, (site) => site.species.symbol === symbol);\n}\n","import { determinant } from \"../matrix/operations/determinant\";\nimport { Lattice } from \"./lattice\";\n\n/* Compute the unit cell volume as the absolute determinant of the basis. /\nexport function volume(lattice: Lattice): number {\n return Math.abs(determinant(lattice.basis));\n}\n","import { Structure } from \"../structure\";\nimport { volume as latticeVolume } from \"../../lattice/volume\";\n\n/\n Compute the volume of a structure's lattice cell.\n * @param structure - Structure to evaluate.\n * @returns Volume in Ang^3.\n /\nexport function volume(structure: Structure): number {\n return latticeVolume(structure.lattice);\n}\n","// NOTE: DISCUSS IF THIS THIS SHOULD BE ALL BUNDLED IN THE mc-periodic-table package.\n// WE CAN REEXPORT FROM THERE,\n\n/* Element metadata from the periodic table. /\nexport interface ElementInfo {\n atomicNumber: number;\n symbol: string;\n name: string;\n mass: number;\n [key: string]: unknown;\n}\n\n/* Atomic-number-keyed periodic table of all known elements. /\nexport const PeriodicTable: Record<number, ElementInfo> = {\n 1: { atomicNumber: 1, symbol: \"H\", name: \"Hydrogen\", mass: 1.008 },\n 2: { atomicNumber: 2, symbol: \"He\", name: \"Helium\", mass: 4.0026 },\n 3: { atomicNumber: 3, symbol: \"Li\", name: \"Lithium\", mass: 6.94 },\n 4: { atomicNumber: 4, symbol: \"Be\", name: \"Beryllium\", mass: 9.0122 },\n 5: { atomicNumber: 5, symbol: \"B\", name: \"Boron\", mass: 10.81 },\n 6: { atomicNumber: 6, symbol: \"C\", name: \"Carbon\", mass: 12.011 },\n 7: { atomicNumber: 7, symbol: \"N\", name: \"Nitrogen\", mass: 14.007 },\n 8: { atomicNumber: 8, symbol: \"O\", name: \"Oxygen\", mass: 15.999 },\n 9: { atomicNumber: 9, symbol: \"F\", name: \"Fluorine\", mass: 18.998 },\n 10: { atomicNumber: 10, symbol: \"Ne\", name: \"Neon\", mass: 20.18 },\n 11: { atomicNumber: 11, symbol: \"Na\", name: \"Sodium\", mass: 22.99 },\n 12: { atomicNumber: 12, symbol: \"Mg\", name: \"Magnesium\", mass: 24.305 },\n 13: { atomicNumber: 13, symbol: \"Al\", name: \"Aluminum\", mass: 26.982 },\n 14: { atomicNumber: 14, symbol: \"Si\", name: \"Silicon\", mass: 28.085 },\n 15: { atomicNumber: 15, symbol: \"P\", name: \"Phosphorus\", mass: 30.974 },\n 16: { atomicNumber: 16, symbol: \"S\", name: \"Sulfur\", mass: 32.06 },\n 17: { atomicNumber: 17, symbol: \"Cl\", name: \"Chlorine\", mass: 35.45 },\n 18: { atomicNumber: 18, symbol: \"Ar\", name: \"Argon\", mass: 39.948 },\n 19: { atomicNumber: 19, symbol: \"K\", name: \"Potassium\", mass: 39.098 },\n 20: { atomicNumber: 20, symbol: \"Ca\", name: \"Calcium\", mass: 40.078 },\n 21: { atomicNumber: 21, symbol: \"Sc\", name: \"Scandium\", mass: 44.956 },\n 22: { atomicNumber: 22, symbol: \"Ti\", name: \"Titanium\", mass: 47.867 },\n 23: { atomicNumber: 23, symbol: \"V\", name: \"Vanadium\", mass: 50.942 },\n 24: { atomicNumber: 24, symbol: \"Cr\", name: \"Chromium\", mass: 51.996 },\n 25: { atomicNumber: 25, symbol: \"Mn\", name: \"Manganese\", mass: 54.938 },\n 26: { atomicNumber: 26, symbol: \"Fe\", name: \"Iron\", mass: 55.845 },\n 27: { atomicNumber: 27, symbol: \"Co\", name: \"Cobalt\", mass: 58.933 },\n 28: { atomicNumber: 28, symbol: \"Ni\", name: \"Nickel\", mass: 58.693 },\n 29: { atomicNumber: 29, symbol: \"Cu\", name: \"Copper\", mass: 63.546 },\n 30: { atomicNumber: 30, symbol: \"Zn\", name: \"Zinc\", mass: 65.38 },\n 31: { atomicNumber: 31, symbol: \"Ga\", name: \"Gallium\", mass: 69.723 },\n 32: { atomicNumber: 32, symbol: \"Ge\", name: \"Germanium\", mass: 72.63 },\n 33: { atomicNumber: 33, symbol: \"As\", name: \"Arsenic\", mass: 74.922 },\n 34: { atomicNumber: 34, symbol: \"Se\", name: \"Selenium\", mass: 78.971 },\n 35: { atomicNumber: 35, symbol: \"Br\", name: \"Bromine\", mass: 79.904 },\n 36: { atomicNumber: 36, symbol: \"Kr\", name: \"Krypton\", mass: 83.798 },\n 37: { atomicNumber: 37, symbol: \"Rb\", name: \"Rubidium\", mass: 85.468 },\n 38: { atomicNumber: 38, symbol: \"Sr\", name: \"Strontium\", mass: 87.62 },\n 39: { atomicNumber: 39, symbol: \"Y\", name: \"Yttrium\", mass: 88.906 },\n 40: { atomicNumber: 40, symbol: \"Zr\", name: \"Zirconium\", mass: 91.224 },\n 41: { atomicNumber: 41, symbol: \"Nb\", name: \"Niobium\", mass: 92.906 },\n 42: { atomicNumber: 42, symbol: \"Mo\", name: \"Molybdenum\", mass: 95.95 },\n 43: { atomicNumber: 43, symbol: \"Tc\", name: \"Technetium\", mass: 98 },\n 44: { atomicNumber: 44, symbol: \"Ru\", name: \"Ruthenium\", mass: 101.07 },\n 45: { atomicNumber: 45, symbol: \"Rh\", name: \"Rhodium\", mass: 102.91 },\n 46: { atomicNumber: 46, symbol: \"Pd\", name: \"Palladium\", mass: 106.42 },\n 47: { atomicNumber: 47, symbol: \"Ag\", name: \"Silver\", mass: 107.868 },\n 48: { atomicNumber: 48, symbol: \"Cd\", name: \"Cadmium\", mass: 112.414 },\n 49: { atomicNumber: 49, symbol: \"In\", name: \"Indium\", mass: 114.818 },\n 50: { atomicNumber: 50, symbol: \"Sn\", name: \"Tin\", mass: 118.71 },\n 51: { atomicNumber: 51, symbol: \"Sb\", name: \"Antimony\", mass: 121.76 },\n 52: { atomicNumber: 52, symbol: \"Te\", name: \"Tellurium\", mass: 127.6 },\n 53: { atomicNumber: 53, symbol: \"I\", name: \"Iodine\", mass: 126.904 },\n 54: { atomicNumber: 54, symbol: \"Xe\", name: \"Xenon\", mass: 131.293 },\n 55: { atomicNumber: 55, symbol: \"Cs\", name: \"Cesium\", mass: 132.905 },\n 56: { atomicNumber: 56, symbol: \"Ba\", name: \"Barium\", mass: 137.33 },\n 57: { atomicNumber: 57, symbol: \"La\", name: \"Lanthanum\", mass: 138.905 },\n 58: { atomicNumber: 58, symbol: \"Ce\", name: \"Cerium\", mass: 140.12 },\n 59: { atomicNumber: 59, symbol: \"Pr\", name: \"Praseodymium\", mass: 140.91 },\n 60: { atomicNumber: 60, symbol: \"Nd\", name: \"Neodymium\", mass: 144.24 },\n 61: { atomicNumber: 61, symbol: \"Pm\", name: \"Promethium\", mass: 145 },\n 62: { atomicNumber: 62, symbol: \"Sm\", name: \"Samarium\", mass: 150.36 },\n 63: { atomicNumber: 63, symbol: \"Eu\", name: \"Europium\", mass: 151.964 },\n 64: { atomicNumber: 64, symbol: \"Gd\", name: \"Gadolinium\", mass: 157.25 },\n 65: { atomicNumber: 65, symbol: \"Tb\", name: \"Terbium\", mass: 158.93 },\n 66: { atomicNumber: 66, symbol: \"Dy\", name: \"Dysprosium\", mass: 162.5 },\n 67: { atomicNumber: 67, symbol: \"Ho\", name: \"Holmium\", mass: 164.93 },\n 68: { atomicNumber: 68, symbol: \"Er\", name: \"Erbium\", mass: 167.26 },\n 69: { atomicNumber: 69, symbol: \"Tm\", name: \"Thulium\", mass: 168.93 },\n 70: { atomicNumber: 70, symbol: \"Yb\", name: \"Ytterbium\", mass: 173.05 },\n 71: { atomicNumber: 71, symbol: \"Lu\", name: \"Lutetium\", mass: 174.97 },\n 72: { atomicNumber: 72, symbol: \"Hf\", name: \"Hafnium\", mass: 178.49 },\n 73: { atomicNumber: 73, symbol: \"Ta\", name: \"Tantalum\", mass: 180.95 },\n 74: { atomicNumber: 74, symbol: \"W\", name: \"Tungsten\", mass: 183.84 },\n 75: { atomicNumber: 75, symbol: \"Re\", name: \"Rhenium\", mass: 186.207 },\n 76: { atomicNumber: 76, symbol: \"Os\", name: \"Osmium\", mass: 190.23 },\n 77: { atomicNumber: 77, symbol: \"Ir\", name: \"Iridium\", mass: 192.217 },\n 78: { atomicNumber: 78, symbol: \"Pt\", name: \"Platinum\", mass: 195.084 },\n 79: { atomicNumber: 79, symbol: \"Au\", name: \"Gold\", mass: 196.967 },\n 80: { atomicNumber: 80, symbol: \"Hg\", name: \"Mercury\", mass: 200.592 },\n 81: { atomicNumber: 81, symbol: \"Tl\", name: \"Thallium\", mass: 204.38 },\n 82: { atomicNumber: 82, symbol: \"Pb\", name: \"Lead\", mass: 207.2 },\n 83: { atomicNumber: 83, symbol: \"Bi\", name: \"Bismuth\", mass: 208.98 },\n 84: { atomicNumber: 84, symbol: \"Po\", name: \"Polonium\", mass: 209 },\n 85: { atomicNumber: 85, symbol: \"At\", name: \"Astatine\", mass: 210 },\n 86: { atomicNumber: 86, symbol: \"Rn\", name: \"Radon\", mass: 222 },\n 87: { atomicNumber: 87, symbol: \"Fr\", name: \"Francium\", mass: 223 },\n 88: { atomicNumber: 88, symbol: \"Ra\", name: \"Radium\", mass: 226 },\n 89: { atomicNumber: 89, symbol: \"Ac\", name: \"Actinium\", mass: 227 },\n 90: { atomicNumber: 90, symbol: \"Th\", name: \"Thorium\", mass: 232.04 },\n 91: { atomicNumber: 91, symbol: \"Pa\", name: \"Protactinium\", mass: 231.04 },\n 92: { atomicNumber: 92, symbol: \"U\", name: \"Uranium\", mass: 238.03 },\n 93: { atomicNumber: 93, symbol: \"Np\", name: \"Neptunium\", mass: 237 },\n 94: { atomicNumber: 94, symbol: \"Pu\", name: \"Plutonium\", mass: 244 },\n 95: { atomicNumber: 95, symbol: \"Am\", name: \"Americium\", mass: 243 },\n 96: { atomicNumber: 96, symbol: \"Cm\", name: \"Curium\", mass: 247 },\n 97: { atomicNumber: 97, symbol: \"Bk\", name: \"Berkelium\", mass: 247 },\n 98: { atomicNumber: 98, symbol: \"Cf\", name: \"Californium\", mass: 251 },\n 99: { atomicNumber: 99, symbol: \"Es\", name: \"Einsteinium\", mass: 252 },\n 100: { atomicNumber: 100, symbol: \"Fm\", name: \"Fermium\", mass: 257 },\n 101: { atomicNumber: 101, symbol: \"Md\", name: \"Mendelevium\", mass: 258 },\n 102: { atomicNumber: 102, symbol: \"No\", name: \"Nobelium\", mass: 259 },\n 103: { atomicNumber: 103, symbol: \"Lr\", name: \"Lawrencium\", mass: 262 },\n 104: { atomicNumber: 104, symbol: \"Rf\", name: \"Rutherfordium\", mass: 267 },\n 105: { atomicNumber: 105, symbol: \"Db\", name: \"Dubnium\", mass: 270 },\n 106: { atomicNumber: 106, symbol: \"Sg\", name: \"Seaborgium\", mass: 269 },\n 107: { atomicNumber: 107, symbol: \"Bh\", name: \"Bohrium\", mass: 270 },\n 108: { atomicNumber: 108, symbol: \"Hs\", name: \"Hassium\", mass: 277 },\n 109: { atomicNumber: 109, symbol: \"Mt\", name: \"Meitnerium\", mass: 278 },\n 110: { atomicNumber: 110, symbol: \"Ds\", name: \"Darmstadtium\", mass: 281 },\n 111: { atomicNumber: 111, symbol: \"Rg\", name: \"Roentgenium\", mass: 282 },\n 112: { atomicNumber: 112, symbol: \"Cn\", name: \"Copernicium\", mass: 285 },\n 113: { atomicNumber: 113, symbol: \"Nh\", name: \"Nihonium\", mass: 286 },\n 114: { atomicNumber: 114, symbol: \"Fl\", name: \"Flerovium\", mass: 289 },\n 115: { atomicNumber: 115, symbol: \"Mc\", name: \"Moscovium\", mass: 289 },\n 116: { atomicNumber: 116, symbol: \"Lv\", name: \"Livermorium\", mass: 293 },\n 117: { atomicNumber: 117, symbol: \"Ts\", name: \"Tennessine\", mass: 294 },\n 118: { atomicNumber: 118, symbol: \"Og\", name: \"Oganesson\", mass: 294 },\n};\n\n/* Symbol-keyed element lookup, derived from PeriodicTable. /\nexport const elementBySymbol = Object.values(PeriodicTable).reduce(\n (acc, el) => {\n acc[el.symbol] = el;\n return acc;\n },\n {} as Record<string, ElementInfo>,\n);\n\n/* Look up an element by its chemical symbol.\n * @param symbol - Element symbol (e.g. \"Fe\")\n * @returns The matching ElementInfo, or undefined if not found. /\nexport function getElement(symbol: string): ElementInfo \| undefined {\n return elementBySymbol[symbol];\n}\n\n/\n Symbol → atomic number lookup (fast + safe)\n /\nexport const SymbolToAtomicNumber = new Map<string, number>(\n Object.values(PeriodicTable).map((el) => [el.symbol, el.atomicNumber]),\n);\n\n/* Atomic-number-to-symbol lookup map. /\nexport const AtomicNumberToSymbol = new Map<number, string>(\n Object.values(PeriodicTable).map((el) => [el.atomicNumber, el.symbol]),\n);\n","import { Structure } from \"../structure\";\nimport { Site } from \"../../site/site\";\nimport { getElement } from \"@/core/data/periodictable/atomicData\";\n\nfunction siteMass(site: Site): number {\n const siteMass = site.properties?.mass;\n\n if (typeof siteMass === \"number\") {\n return siteMass;\n }\n\n const speciesMass = site.species.properties?.mass;\n\n if (typeof speciesMass === \"number\") {\n return speciesMass;\n }\n\n const element = getElement(site.species.symbol);\n\n if (!element) {\n throw new Error(`Unknown element: ${site.species.symbol}`);\n }\n\n return element.mass;\n}\n\n/\n Sum the masses of all sites in the structure.\n * @param structure - Structure to evaluate.\n * @returns Total mass in atomic mass units.\n /\nexport function cellMass(structure: Structure): number {\n let mass = 0;\n\n for (const site of structure.sites) {\n mass += siteMass(site);\n }\n\n return mass;\n}\n","import { Structure } from \"../structure\";\nimport { volume } from \"./volume\";\nimport { cellMass } from \"./cellMass\";\n\n/\n Compute the density of a structure.\n * @param structure - Structure to evaluate.\n * @returns Density in amu/Ang^3.\n /\nexport function density(structure: Structure): number {\n const vol = volume(structure);\n\n if (vol < 1e-300) {\n throw new Error(\"Degenerate cell has no volume\");\n }\n\n return cellMass(structure) / vol;\n}\n","import { Structure } from \"../structure\";\nimport { Species } from \"../../species/species\";\n\n/\n Collect unique Species from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of unique Species.\n /\nexport function getSpecies(structure: Structure): Species[] {\n const species = new Map<string, Species>();\n\n for (const site of structure.sites) {\n const key = site.species.symbol;\n\n if (!species.has(key)) {\n species.set(key, site.species);\n }\n }\n\n return Array.from(species.values());\n}\n\n/\n Collect unique element symbols from a structure.\n * @param structure - Structure to evaluate.\n * @returns Array of element symbols.\n /\nexport function getElements(structure: Structure): string[] {\n return getSpecies(structure).map((s) => s.symbol);\n}\n\n/\n Count occurrences of each species symbol in a structure.\n * @param structure - Structure to evaluate.\n * @returns Map of element symbols to occurrence counts.\n /\nexport function getSpeciesCounts(structure: Structure): Map<string, number> {\n const counts = new Map<string, number>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n counts.set(symbol, (counts.get(symbol) ?? 0) + 1);\n }\n\n return counts;\n}\n","import { Species } from \"../species/species\";\n\n/* Generic site properties map. /\nexport type SiteProperties = Record<string, any>;\n\n/* A 3D vector type. /\nexport type Vec3 = [number, number, number] \| Float64Array \| number[];\n\n/* A site with a species, fractional coordinates, and optional properties. /\nexport type Site<P extends SiteProperties = SiteProperties> = {\n species: Species;\n frac: Vec3;\n properties?: P;\n};\n\n/* Create a new Site object.\n * @param species - The species at the site.\n * @param frac - Fractional coordinates.\n * @param properties - Optional properties.\n * @returns A new Site. /\nexport function createSite<P extends SiteProperties>(\n species: Species,\n frac: Vec3,\n properties?: P,\n): Site<P> {\n return {\n species,\n frac,\n properties,\n };\n}\n","import { Lattice } from \"../lattice/lattice\";\nimport { Site } from \"./site\";\nimport { cartesian } from \"./cartesian\";\n\nimport { norm } from \"../matrix/operations/vector/norm\";\n\n/* Compute the minimum image distance between two sites.\n * @param lattice - The lattice.\n * @param a - First site.\n * @param b - Second site.\n * @returns Minimum image distance. /\nexport function distance(lattice: Lattice, a: Site, b: Site): number {\n const dFrac: [number, number, number] = [\n b.frac[0] - a.frac[0],\n b.frac[1] - a.frac[1],\n b.frac[2] - a.frac[2],\n ];\n\n for (let i = 0; i < 3; i++) {\n dFrac[i] -= Math.round(dFrac[i]);\n }\n\n const displaced: Site = {\n species: a.species,\n frac: dFrac,\n };\n\n const dCart = cartesian(lattice, displaced);\n\n return norm(dCart);\n}\n","import { Site, SiteProperties } from \"./site\";\n\nfunction wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n}\n\n/* Wrap a site's fractional coordinates into [0, 1).\n * @param site - The site to wrap.\n * @returns A new site with wrapped coordinates. /\nexport function wrap<T extends SiteProperties>(site: Site<T>): Site<T> {\n return {\n ...site,\n frac: [\n wrapValue(site.frac[0]),\n wrapValue(site.frac[1]),\n wrapValue(site.frac[2]),\n ],\n };\n}\n","/* A chemical species with a symbol and optional properties. /\nexport type Species<P extends Record<string, any> = Record<string, any>> = {\n symbol: string;\n properties?: P;\n};\n\n/* Create a new Species.\n * @param symbol - Element symbol.\n * @param properties - Optional properties.\n * @returns A new Species. /\nexport function createSpecies<P extends Record<string, any>>(\n symbol: string,\n properties?: P,\n): Species<P> {\n return { symbol, properties };\n}\n","export type {\n KPoints,\n KPath,\n KPoint,\n KPointSet,\n KGrid,\n Vec3,\n GridShape,\n} from \"./kpoints\";\n","import { Matrix } from \"../matrix\";\nimport { identity } from \"../matrix\";\n\n/* Scalar or multi-channel volumetric grid data. /\nexport interface VolumetricData {\n readonly data: Float64Array;\n readonly shape: [number, number, number];\n readonly channels: number;\n readonly basis?: Matrix;\n readonly origin: [number, number, number];\n readonly field?: string;\n readonly metadata?: Record<string, unknown>;\n}\n\ntype ReduceAxis = \"all\" \| \"channels\";\n\n/* Reduction axis configuration. /\nexport interface ReduceOptions {\n axis?: ReduceAxis;\n}\n\n/* Create a VolumetricData from shape and optional data buffer. /\nexport function createVolumetricData(params: {\n shape: [number, number, number];\n channels?: number;\n\n /\n Flat voxel-major buffer.\n \n Layout:\n * [v000c0, v000c1, ..., v001c0, v001c1, ...]\n /\n data?: Float64Array \| Iterable<number>;\n\n basis?: Matrix;\n origin?: [number, number, number];\n\n field?: string;\n metadata?: Record<string, unknown>;\n}): VolumetricData {\n const {\n shape,\n channels = 1,\n data,\n basis,\n origin = [0, 0, 0],\n field,\n metadata,\n } = params;\n\n const [D, H, W] = shape;\n const size = D H * W * channels;\n\n const buffer =\n data instanceof Float64Array\n ? data\n : data\n ? Float64Array.from(data)\n : new Float64Array(size);\n\n if (buffer.length !== size) {\n throw new Error(\n `VolumetricData mismatch: expected ${size}, got ${buffer.length}`,\n );\n }\n\n return {\n data: buffer,\n shape,\n channels,\n basis: basis ?? identity(3),\n origin,\n field,\n metadata,\n };\n}\n\n/** Compute the flat buffer index for a voxel coordinate and channel. /\n/* * Performance-critical inner loops should generally use direct offset arithmetic.\n/** @param vol - Volumetric data. /\n/* @param x - Column index. /\n/* @param y - Row index. /\n/* @param z - Depth index. /\n/* @param c - Channel index. /\n/* @returns Linear index into the data buffer. /\nexport function index(\n vol: VolumetricData,\n x: number,\n y: number,\n z: number,\n c: number,\n) {\n const [D, H, W] = vol.shape;\n const { channels } = vol;\n\n return ((z H + y) * W + x) * channels + c;\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Create a volumetric grid filled with a constant value. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param value - Fill value. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData filled with value. /\nexport function fill(\n shape: [number, number, number],\n value: number,\n channels = 1,\n) {\n const size = shape[0] shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size).fill(value),\n });\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/** Generate volumetric data by evaluating a function over every voxel and channel. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param fn - Callback receiving (x, y, z, c) returning the value at that voxel. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData populated by fn. /\nexport function fromFunction(\n shape: [number, number, number],\n fn: (x: number, y: number, z: number, c: number) => number,\n channels = 1,\n) {\n const [D, H, W] = shape;\n const data = new Float64Array(D H * W * channels);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n for (let y = 0; y < H; y++) {\n for (let x = 0; x < W; x++) {\n for (let c = 0; c < channels; c++) {\n data[i++] = fn(x, y, z, c);\n }\n }\n }\n }\n\n return createVolumetricData({\n shape,\n channels,\n data,\n });\n}\n","import { Matrix } from \"../../matrix\";\nimport { createVolumetricData } from \"../volumetric\";\n\n/** Stack a list of 2-D Matrix slices into a 3-D volumetric grid. /\n/* @param slices - Array of matrices (depth dimension). /\n/* @returns A new VolumetricData with shape [slices.length, H, W]. /\nexport function fromMatrixSlices(slices: Matrix[]) {\n if (slices.length === 0) {\n throw new Error(\"No slices provided\");\n }\n\n const H = slices[0].rows;\n const W = slices[0].cols;\n const D = slices.length;\n\n const data = new Float64Array(D H * W);\n\n let i = 0;\n\n for (let z = 0; z < D; z++) {\n const m = slices[z];\n\n if (m.rows !== H \|\| m.cols !== W) {\n throw new Error(\"Inconsistent matrix slice dimensions\");\n }\n\n data.set(m.data, i);\n i += m.data.length;\n }\n\n return createVolumetricData({\n shape: [D, H, W],\n data,\n });\n}\n","import { fill } from \"./fill\";\n\n/** Create a volumetric grid filled with ones. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData with all values set to 1. /\nexport function ones(shape: [number, number, number], channels = 1) {\n return fill(shape, 1, channels);\n}\n","import { createVolumetricData } from \"../volumetric\";\n\n/* Create a volumetric grid filled with zeros. /\n/* @param shape - Grid dimensions [depth, height, width]. /\n/* @param channels - Number of channels (default 1). /\n/* @returns A new VolumetricData with all values set to 0. /\nexport function zeros(shape: [number, number, number], channels = 1) {\n const size = shape[0] shape[1] * shape[2] * channels;\n\n return createVolumetricData({\n shape,\n channels,\n data: new Float64Array(size),\n });\n}\n","export interface SymmetryOperation {\n matrix: number[][];\n translation: number[];\n}\n\nfunction parseFraction(s: string): number {\n const trimmed = s.trim();\n\n if (trimmed.includes(\"/\")) {\n const [num, den] = trimmed.split(\"/\").map(Number);\n return num / den;\n }\n\n return Number(trimmed);\n}\n\nfunction parseComponent(expr: string): { coeffs: number[]; offset: number } {\n const cleaned = expr.replace(/\\s+/g, \"\");\n let offset = 0;\n const coeffs = [0, 0, 0];\n\n const terms = cleaned.match(/[+-]?[^+-]+/g) ?? [];\n\n const VAR_INDEX: Record<string, number> = { x: 0, y: 1, z: 2 };\n\n for (const term of terms) {\n const t = term.trim();\n\n if (t.length > 0 && VAR_INDEX[t.at(-1)!] !== undefined) {\n const idx = VAR_INDEX[t.at(-1)!];\n const sign = t.startsWith(\"-\") ? -1 : 1;\n\n coeffs[idx] += sign;\n } else {\n const frac = t.match(/([+-]?\\d+\\s\\/\\s\\d+)/);\n\n if (frac) {\n offset += parseFraction(frac[1].replace(/\\s/g, \"\"));\n } else {\n const val = Number(t);\n\n if (!isNaN(val)) {\n offset += val;\n }\n }\n }\n }\n\n return { coeffs, offset };\n}\n\n/** Parse a single symmetry operation string like '-y, x, z+1/2' into a matrix + translation.\n * @param op - The operation string (e.g. '-y, x, z+1/2').\n * @returns A SymmetryOperation with 3x3 matrix and translation vector. /\nexport function parseOperation(op: string): SymmetryOperation {\n const components = op.split(\",\").map((s) => parseComponent(s));\n\n return {\n matrix: components.map((c) => c.coeffs),\n translation: components.map((c) => c.offset),\n };\n}\n\n/* Parse all symmetry operation strings from a CIF _symmetry_equiv_pos_as_xyz loop.\n * @param ops - Array of operation strings (e.g. [\"x, y, z\", \"-x, -y, z\"]).\n * @returns Array of SymmetryOperation objects. /\nexport function parseOperations(ops: string[]): SymmetryOperation[] {\n return ops.map(parseOperation);\n}\n\n/* Apply a symmetry operation to fractional coordinates.\n * @param op - The symmetry operation.\n * @param frac - Fractional coordinates [x, y, z].\n * * @returns New fractional coordinates after applying the operation. /\nexport function applyOperation(\n op: SymmetryOperation,\n frac: number[],\n): number[] {\n const result = [0, 0, 0];\n\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n result[i] += op.matrix[i][j] frac[j];\n }\n\n result[i] += op.translation[i];\n }\n\n return result;\n}\n","/*\n Reads lines from a string one at a time, without pre-splitting into an array.\n /\nexport class LineReader {\n private pos = 0;\n /* Number of lines returned so far (including blank lines). /\n count = 0;\n\n constructor(private readonly text: string) {}\n\n /* Return the next line (without the newline character), or `null` at EOF. /\n next(): string \| null {\n if (this.pos >= this.text.length) return null;\n const end = this.text.indexOf(\"\\n\", this.pos);\n const line = end === -1 ? this.text.slice(this.pos) : this.text.slice(this.pos, end);\n this.pos = end === -1 ? this.text.length : end + 1;\n this.count++;\n return line;\n }\n\n /* Return a trimmed line, or throw on unexpected EOF. /\n nextTrimmed(): string {\n const line = this.next();\n if (line === null) throw new Error(\"Unexpected EOF\");\n return line.trim();\n }\n}\n","import { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { parameters } from \"../../lattice/parameters\";\nimport { Structure } from \"../../structure/structure\";\nimport {\n parseOperations,\n applyOperation,\n} from \"./symmetryOperations\";\nimport { LineReader } from \"../helpers\";\n\nfunction cleanValue(value: string \| undefined): number {\n if (value === undefined) return NaN;\n\n const unquoted = value.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n // remove uncertainty notation:\n // 5.432(1) -> 5.432\n return Number(unquoted.replace(/\$.+\$/, \"\"));\n}\n\nfunction tokenize(line: string): string[] {\n return line.match(/'[^']'\|\"[^\"]\"\|\\S+/g) ?? [];\n}\n\nfunction isSymOpHeader(header: string): boolean {\n const t = header.toLowerCase();\n return (\n t.includes(\"symmetry_equiv_pos\") \|\| t.includes(\"symop_operation_xyz\")\n );\n}\n\n/* Strips oxidation-state/charge suffixes (e.g. \"Na1+\" -> \"Na\", \"O2-\" -> \"O\"). /\nfunction cleanSpeciesSymbol(raw: string \| undefined): string {\n if (raw === undefined) return \"\";\n const unquoted = raw.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n const m = unquoted.match(/^([A-Z][a-z]?)/);\n return m ? m[1] : unquoted;\n}\n\n/* Parses a CIF (Crystallographic Information File) string into a Structure. /\nexport function fromCIF(text: string): Structure {\n let a = 0;\n let b = 0;\n let c = 0;\n\n let alpha = 0;\n let beta = 0;\n let gamma = 0;\n\n let atomHeaders: string[] = [];\n const atomRows: string[][] = [];\n\n let inLoop = false;\n let currentHeaders: string[] = [];\n let collectingAtoms = false;\n let collectingSymOps = false;\n // Headers mention atom sites but the loop kind is only known once data\n // starts (coordinate loop vs. aniso/geom/etc.). Resolved per loop.\n let potentialAtoms = false;\n let loopIsAniso = false;\n const symOpStrings: string[] = [];\n\n function resetLoopState() {\n inLoop = false;\n collectingAtoms = false;\n collectingSymOps = false;\n potentialAtoms = false;\n loopIsAniso = false;\n currentHeaders = [];\n }\n\n const r = new LineReader(text);\n let rawLine: string \| null;\n while ((rawLine = r.next()) !== null) {\n const line = rawLine.trim();\n if (!line) continue;\n\n // Comments and data/save blocks always terminate an active loop.\n if (line.startsWith(\"#\")) continue;\n if (line.startsWith(\"data_\") \|\| line.startsWith(\"save_\")) {\n resetLoopState();\n continue;\n }\n\n if (line === \"loop_\") {\n inLoop = true;\n currentHeaders = [];\n collectingAtoms = false;\n collectingSymOps = false;\n potentialAtoms = false;\n loopIsAniso = false;\n continue;\n }\n\n if (line.startsWith(\"_cell_length_a\")) {\n a = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_b\")) {\n b = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_length_c\")) {\n c = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_alpha\")) {\n alpha = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_beta\")) {\n beta = cleanValue(tokenize(line)[1]);\n } else if (line.startsWith(\"_cell_angle_gamma\")) {\n gamma = cleanValue(tokenize(line)[1]);\n }\n\n if (inLoop && line.startsWith(\"_\")) {\n // A tag after data rows have started belongs outside the loop:\n // terminate the loop and treat it as a regular tag line.\n if (atomRows.length > 0 && collectingAtoms) {\n resetLoopState();\n continue;\n }\n if (symOpStrings.length > 0 && collectingSymOps) {\n resetLoopState();\n continue;\n }\n\n currentHeaders.push(line);\n\n if (isSymOpHeader(line)) {\n collectingSymOps = true;\n collectingAtoms = false;\n potentialAtoms = false;\n } else if (line.includes(\"_atom_site_aniso_\")) {\n // Anisotropic displacement parameters for the same sites —\n // never coordinate data.\n loopIsAniso = true;\n collectingAtoms = false;\n potentialAtoms = false;\n } else if (line.includes(\"_atom_site_\")) {\n // Could be the coordinate loop, but also matches geom loops\n // (e.g. `_geom_angle_atom_site_label_1`). Decided at data time.\n if (!loopIsAniso) potentialAtoms = true;\n collectingSymOps = false;\n }\n\n continue;\n }\n\n if (inLoop && potentialAtoms && !collectingAtoms) {\n // First data row of a candidate atom loop: only coordinate loops\n // (with fractional columns) are collected; aniso/geom/etc. ignored.\n const hasFract =\n currentHeaders.some((h) => h.includes(\"fract_x\")) \|\|\n currentHeaders.some((h) => h.includes(\"fract_y\")) \|\|\n currentHeaders.some((h) => h.includes(\"fract_z\"));\n\n if (!hasFract \|\| loopIsAniso) {\n potentialAtoms = false;\n } else {\n potentialAtoms = false;\n collectingAtoms = true;\n collectingSymOps = false;\n }\n }\n\n if (inLoop && collectingAtoms) {\n if (atomHeaders.length === 0) {\n atomHeaders = [...currentHeaders];\n }\n\n atomRows.push(tokenize(line));\n }\n\n if (inLoop && collectingSymOps) {\n // Symop rows look like `12 'x+1/2, y, -z'` or `x, y, z`.\n // Parse the whole line instead of individual tokens so unquoted\n // operations are not split apart.\n let s = line;\n const idMatch = s.match(/^\\d+\\s+(.)$/);\n if (idMatch) s = idMatch[1].trim();\n s = s.replace(/^['\"]+\|['\"]+$/g, \"\").trim();\n\n if (s.includes(\",\")) {\n symOpStrings.push(s);\n }\n }\n }\n\n const lattice = fromParameters(a, b, c, alpha, beta, gamma);\n\n const ix = atomHeaders.findIndex((x) => x.includes(\"fract_x\"));\n\n const iy = atomHeaders.findIndex((x) => x.includes(\"fract_y\"));\n\n const iz = atomHeaders.findIndex((x) => x.includes(\"fract_z\"));\n\n const ispecies = atomHeaders.findIndex((x) => x.includes(\"type_symbol\"));\n\n if (ix < 0 \|\| iy < 0 \|\| iz < 0 \|\| ispecies < 0) {\n throw new Error(\"Missing required atom site columns\");\n }\n\n const maxCol = Math.max(ix, iy, iz, ispecies);\n\n const asymSites = atomRows.map((row) => {\n if (row.length <= maxCol) {\n throw new Error(\"Incomplete atom site data row\");\n }\n\n return {\n species: {\n symbol: cleanSpeciesSymbol(row[ispecies]),\n },\n\n frac: new Float64Array([\n cleanValue(row[ix]),\n cleanValue(row[iy]),\n cleanValue(row[iz]),\n ]),\n };\n });\n\n if (symOpStrings.length === 0) {\n return { lattice, sites: asymSites };\n }\n\n const symOps = parseOperations(symOpStrings);\n\n const EPS = 1e-3;\n\n function wrapValue(x: number): number {\n return ((x % 1) + 1) % 1;\n }\n\n function cleanNearZero(x: number): number {\n return Math.abs(x) < EPS ? 0 : x;\n }\n\n function posKey(species: string, frac: number[]): string {\n const w = frac.map((v) => {\n const c = cleanNearZero(wrapValue(v));\n return Math.round(c * 1000) / 1000;\n });\n\n return `${species}:${w[0]},${w[1]},${w[2]}`;\n }\n\n const seen = new Set<string>();\n const sites: { species: { symbol: string }; frac: Float64Array }[] = [];\n\n for (const site of asymSites) {\n for (const op of symOps) {\n const operated = applyOperation(op, Array.from(site.frac));\n\n const frac = [\n cleanNearZero(wrapValue(operated[0])),\n cleanNearZero(wrapValue(operated[1])),\n cleanNearZero(wrapValue(operated[2])),\n ];\n\n const key = posKey(site.species.symbol, frac);\n\n if (!seen.has(key)) {\n seen.add(key);\n\n sites.push({\n species: { symbol: site.species.symbol },\n frac: new Float64Array(frac),\n });\n }\n }\n }\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a CIF string. /\nexport function toCIF(structure: Structure, precision = 6): string {\n const p = parameters(structure.lattice);\n\n const lines: string[] = [];\n\n lines.push(\"data_matsci-parse\");\n lines.push(\"\");\n\n lines.push(\"_symmetry_space_group_name_H-M 'P 1'\");\n lines.push(\"_symmetry_Int_Tables_number 1\");\n\n lines.push(\"\");\n\n lines.push(`_cell_length_a ${p[0].toFixed(precision)}`);\n\n lines.push(`_cell_length_b ${p[1].toFixed(precision)}`);\n\n lines.push(`_cell_length_c ${p[2].toFixed(precision)}`);\n\n lines.push(`_cell_angle_alpha ${p[3].toFixed(precision)}`);\n\n lines.push(`_cell_angle_beta ${p[4].toFixed(precision)}`);\n\n lines.push(`_cell_angle_gamma ${p[5].toFixed(precision)}`);\n\n lines.push(\"\");\n\n lines.push(\"loop_\");\n lines.push(\"_atom_site_label\");\n lines.push(\"_atom_site_type_symbol\");\n lines.push(\"_atom_site_fract_x\");\n lines.push(\"_atom_site_fract_y\");\n lines.push(\"_atom_site_fract_z\");\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n lines.push(\n `${site.species.symbol}${i + 1} ` +\n `${site.species.symbol} ` +\n `${site.frac[0].toFixed(precision)} ` +\n `${site.frac[1].toFixed(precision)} ` +\n `${site.frac[2].toFixed(precision)}`,\n );\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { cartesian, fractional } from \"../site\";\nimport { LineReader } from \"./helpers\";\n\nfunction isSelective(line: string): boolean {\n return line.toLowerCase().startsWith(\"selective\");\n}\n\nfunction isCartesian(line: string): boolean {\n const l = line.trim().toLowerCase();\n return l.startsWith(\"c\") \|\| l.startsWith(\"k\");\n}\n\n/* Parses a POSCAR/CONTCAR string into a Structure. /\nexport function fromPOSCAR(text: string): Structure {\n const r = new LineReader(text);\n\n // comment/title\n r.next();\n\n // scale factor\n const scale = Number(r.nextTrimmed());\n\n // lattice vectors (row-major)\n const latticeData: number[] = [];\n\n for (let i = 0; i < 3; i++) {\n const v = r.nextTrimmed().split(/\\s+/).map(Number);\n\n if (v.length !== 3) {\n throw new Error(\"Invalid POSCAR lattice\");\n }\n\n latticeData.push(v[0] scale, v[1] * scale, v[2] * scale);\n }\n\n const lattice = createLattice(latticeData);\n\n // VASP5 species names\n const symbols = r.nextTrimmed().split(/\\s+/);\n\n // atom counts\n const counts = r.nextTrimmed().split(/\\s+/).map(Number);\n\n if (symbols.length !== counts.length) {\n throw new Error(\"Species/count mismatch\");\n }\n\n // optional selective dynamics\n let selective = false;\n\n let line = r.nextTrimmed();\n if (isSelective(line)) {\n selective = true;\n line = r.nextTrimmed();\n }\n\n // direct is true unless cartesian is.\n let direct = true;\n direct = !isCartesian(line);\n\n const sites: Site[] = [];\n\n let speciesIndex = 0;\n let remaining = counts[0];\n\n const totalAtoms = counts.reduce((a, b) => a + b, 0);\n\n for (let i = 0; i < totalAtoms; i++) {\n const tokens = r.nextTrimmed().split(/\\s+/);\n\n const coords = tokens.slice(0, 3).map(Number);\n\n const frac = direct\n ? new Float64Array(coords)\n : fractional(lattice, new Float64Array(coords));\n\n const props: Record<string, unknown> = {};\n\n if (selective) {\n const sd = tokens.slice(3, 6).map((t) => t.toLowerCase() === \"t\");\n\n if (sd.length === 3) {\n props.selectiveDynamics = sd as [boolean, boolean, boolean];\n }\n }\n\n sites.push({\n species: {\n symbol: symbols[speciesIndex],\n },\n frac,\n ...(Object.keys(props).length > 0 ? { properties: props } : {}),\n });\n\n remaining--;\n\n if (remaining === 0 && speciesIndex < counts.length - 1) {\n speciesIndex++;\n remaining = counts[speciesIndex];\n }\n }\n\n return {\n lattice,\n sites,\n selectiveDynamics: selective \|\| undefined,\n _cursorEnd: r.count,\n };\n}\n\n/** Serializes a Structure to a POSCAR string. /\nexport function toPOSCAR(\n structure: Structure,\n options?: {\n title?: string;\n scale?: number;\n direct?: boolean;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n const scale = options?.scale ?? 1.0;\n const direct = options?.direct ?? true;\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(scale));\n\n // lattice\n const m = structure.lattice.basis.data;\n\n lines.push(`${m[0]} ${m[1]} ${m[2]}`);\n lines.push(`${m[3]} ${m[4]} ${m[5]}`);\n lines.push(`${m[6]} ${m[7]} ${m[8]}`);\n\n // preserve order of first appearance\n const grouped = new Map<string, typeof structure.sites>();\n\n for (const site of structure.sites) {\n const symbol = site.species.symbol;\n\n const group = grouped.get(symbol);\n\n if (group) {\n group.push(site);\n } else {\n grouped.set(symbol, [site]);\n }\n }\n\n\n const species = [...grouped.keys()];\n const sites = [...grouped.values()].flat();\n\n lines.push(species.join(\" \"));\n lines.push(species.map((s) => (grouped.get(s) ?? []).length).join(\" \"));\n\n const hasSelective = structure.selectiveDynamics ?? sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n lines.push(\"Selective Dynamics\");\n }\n\n lines.push(direct ? \"Direct\" : \"Cartesian\");\n\n for (const site of sites) {\n const coords = direct ? site.frac : cartesian(structure.lattice, site);\n\n let line = `${coords[0]} ${coords[1]} ${coords[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\n/* AiiDA-compatible site representation. /\nexport interface AiiDASite {\n position: [number, number, number];\n kind_name: string[];\n}\n\n/* AiiDA-compatible structure data format. /\nexport interface StructureData {\n cell: [\n [number, number, number],\n [number, number, number],\n [number, number, number],\n ];\n kinds: [];\n sites: AiiDASite[];\n}\n\n/* Parses an AiiDA StructureData object into a Structure. /\nexport function fromStructureData(data: StructureData): Structure {\n const lattice = createLattice([\n ...data.cell[0],\n ...data.cell[1],\n ...data.cell[2],\n ]);\n\n const kindMap = new Map(data.kinds.map((kind: any) => [kind.name, kind]));\n\n const sites = data.sites.map((site: any) => {\n const kind = kindMap.get(site.kind_name);\n\n if (!kind) {\n throw new Error(`Unknown kind \"${site.kind_name}\"`);\n }\n\n return {\n species: {\n symbol: kind.symbols[0],\n },\n\n frac: fractional(lattice, new Float64Array(site.position)),\n };\n });\n\n return {\n lattice,\n sites,\n };\n}\n\n/* Serializes a Structure to an AiiDA StructureData-compatible object. /\nexport function toStructureData(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const symbols = [...new Set(structure.sites.map((s) => s.species.symbol))];\n\n const kinds = symbols.map((symbol) => ({\n name: symbol,\n symbols: [symbol],\n }));\n\n return {\n cell: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n kinds,\n\n sites: structure.sites.map((site) => ({\n kind_name: site.species.symbol,\n\n position: Array.from(cartesian(structure.lattice, site)),\n })),\n\n pbc1: true,\n pbc2: true,\n pbc3: true,\n };\n}\n","import { createLattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site/cartesian\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\nfunction nextSectionLine(r: LineReader, section: string): void {\n let line: string \| null;\n while ((line = r.next()) !== null) {\n if (line.trim().toUpperCase() === section) return;\n }\n throw new Error(`Missing ${section}`);\n}\n\n// TODO: support atomic numbers instead of symbols in primvec.\n\n/* Parses an XSF (XCrySDen Structure Format) string into a Structure. /\nexport function fromXSF(text: string): Structure {\n const r = new LineReader(text);\n\n nextSectionLine(r, \"PRIMVEC\");\n\n const lattice = createLattice([\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ...r.nextTrimmed().split(/\\s+/).map(Number),\n ]);\n\n nextSectionLine(r, \"PRIMCOORD\");\n\n const countLine = r.nextTrimmed();\n const [nAtoms] = countLine.split(/\\s+/).map(Number);\n\n if (!Number.isInteger(nAtoms) \|\| nAtoms < 0) {\n throw new Error(\"Invalid atom count in PRIMCOORD\");\n }\n\n const invData = inverse(lattice).data;\n\n const sites: Site[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const tokens = r.nextTrimmed().split(/\\s+/);\n\n const symbol = tokens[0];\n\n const x = Number(tokens[1]);\n const y = Number(tokens[2]);\n const z = Number(tokens[3]);\n\n sites.push({\n species: { symbol },\n // inlined frac conv for perf.\n frac: new Float64Array([\n invData[0] x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n });\n }\n\n return {\n lattice,\n sites,\n };\n}\n\nfunction formatVec(v: number[]): string {\n return `${v[0]} ${v[1]} ${v[2]}`;\n}\n\nfunction formatLattice(lattice: Structure[\"lattice\"]): string[] {\n const m = lattice.basis.data;\n\n return [\n formatVec([m[0], m[1], m[2]]),\n formatVec([m[3], m[4], m[5]]),\n formatVec([m[6], m[7], m[8]]),\n ];\n}\n\n/** Serializes a Structure to an XSF string. /\nexport function toXSF(structure: Structure): string {\n const lines: string[] = [];\n\n lines.push(\"CRYSTAL\");\n lines.push(\"PRIMVEC\");\n\n const latticeLines = formatLattice(structure.lattice);\n lines.push(...latticeLines);\n lines.push(\"PRIMCOORD\");\n lines.push(`${structure.sites.length} 1`);\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n lines.push(`${site.species.symbol} ${c[0]} ${c[1]} ${c[2]}`);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice, Lattice } from \"../lattice/lattice\";\nimport { inverse } from \"../lattice/inverse\";\nimport { cartesian } from \"../site\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LineReader } from \"./helpers\";\n\ntype ExtendedXYZInfo = Record<string, string>;\n\ntype PropDef = {\n name: string;\n type: string;\n count: number;\n offset: number;\n};\n\nfunction parseHeader(comment: string): ExtendedXYZInfo {\n const info: ExtendedXYZInfo = {};\n const kvRegex = /(\\w+)=(\".?\"\|\\S+)/g;\n\n for (const match of comment.matchAll(kvRegex)) {\n let value = match[2];\n if (value.startsWith('\"')) value = value.slice(1, -1);\n info[match[1]] = value;\n }\n\n return info;\n}\n\nfunction parseLattice(info: ExtendedXYZInfo) {\n if (!info.Lattice) {\n throw new Error(\"Extended XYZ must contain Lattice\");\n }\n\n const v = info.Lattice.split(/\\s+/).map(Number);\n if (v.length !== 9) throw new Error(\"Invalid Lattice\");\n\n return createLattice([v[0], v[1], v[2], v[3], v[4], v[5], v[6], v[7], v[8]]);\n}\n\nfunction parseProperties(propStr: string): PropDef[] {\n const parts = propStr.split(\":\");\n const props: PropDef[] = [];\n let offset = 0;\n\n for (let i = 0; i < parts.length; i += 3) {\n const count = Number(parts[i + 2]);\n props.push({\n name: parts[i],\n type: parts[i + 1],\n count,\n offset,\n });\n offset += count;\n }\n\n return props;\n}\n\n/** Parses an extended XYZ string into a Structure. /\nexport function fromXYZ(text: string): Structure {\n const r = new LineReader(text);\n\n // skip leading blank lines\n let line: string \| null;\n do {\n line = r.next();\n } while (line !== null && line.trim().length === 0);\n\n if (line === null) throw new Error(\"XYZ file is too short\");\n\n const n = Number(line.trim());\n\n if (!Number.isInteger(n) \|\| n < 0) {\n throw new Error(\"Invalid atom count in XYZ file\");\n }\n\n const comment = r.next();\n if (comment === null) throw new Error(\"XYZ file is too short\");\n\n const info = parseHeader(comment);\n const lattice = parseLattice(info);\n\n const propDefs = info.Properties\n ? parseProperties(info.Properties)\n : [\n { name: \"species\", type: \"S\", count: 1, offset: 0 },\n { name: \"pos\", type: \"R\", count: 3, offset: 1 },\n ];\n\n const sites: Site[] = [];\n\n let hasSelective = false;\n\n const invData = inverse(lattice).data;\n\n for (let i = 0; i < n; i++) {\n const atomLine = r.next();\n if (atomLine === null)\n throw new Error(\"Atom count exceeds available lines in XYZ file\");\n\n const tokens = atomLine.trim().split(/\\s+/);\n\n let symbol = \"\";\n let x = 0,\n y = 0,\n z = 0;\n const props: Record<string, unknown> = {};\n\n for (const def of propDefs) {\n const values = tokens.slice(def.offset, def.offset + def.count);\n\n if (def.name === \"species\") {\n symbol = values[0];\n } else if (def.name === \"pos\") {\n x = Number(values[0]);\n y = Number(values[1]);\n z = Number(values[2]);\n } else if (def.name === \"selectiveDynamics\") {\n const sd = values.map((v: string) => v.toLowerCase() === \"t\") as [\n boolean,\n boolean,\n boolean,\n ];\n props.selectiveDynamics = sd;\n hasSelective = true;\n } else {\n if (def.type === \"L\") {\n props[def.name] = values.map((v: string) => v.toLowerCase() === \"t\");\n } else if (def.type === \"R\" \|\| def.type === \"I\") {\n props[def.name] = values.map(Number);\n } else {\n props[def.name] = values.length === 1 ? values[0] : values;\n }\n }\n }\n\n if (!symbol) throw new Error(\"Missing species in XYZ\");\n if (!z && z !== 0) throw new Error(\"Invalid coordinates in XYZ\");\n\n const site: Site = {\n species: { symbol },\n // inlined site conv for perf.\n frac: new Float64Array([\n invData[0] x + invData[3] * y + invData[6] * z,\n invData[1] * x + invData[4] * y + invData[7] * z,\n invData[2] * x + invData[5] * y + invData[8] * z,\n ]),\n };\n\n if (Object.keys(props).length > 0) {\n site.properties = props;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n selectiveDynamics: hasSelective \|\| undefined,\n };\n}\n\nfunction formatLattice(lattice: Lattice): string {\n const m = lattice.basis.data;\n\n return `${m[0]} ${m[1]} ${m[2]} ${m[3]} ${m[4]} ${m[5]} ${m[6]} ${m[7]} ${m[8]}`;\n}\n\n/** Serializes a Structure to an extended XYZ string. /\nexport function toXYZ(structure: Structure): string {\n const lines: string[] = [];\n\n const sites = structure.sites;\n lines.push(String(sites.length));\n\n const latticeStr = formatLattice(structure.lattice);\n\n const propParts: string[] = [\"species\", \"S\", \"1\", \"pos\", \"R\", \"3\"];\n const hasSelective =\n structure.selectiveDynamics ??\n sites.some((s) => s.properties?.selectiveDynamics);\n\n if (hasSelective) {\n propParts.push(\"selectiveDynamics\", \"L\", \"3\");\n }\n\n lines.push(`Lattice=\"${latticeStr}\" Properties=${propParts.join(\":\")}`);\n\n for (const site of sites) {\n const cart = cartesian(structure.lattice, site);\n let line = `${site.species.symbol} ${cart[0]} ${cart[1]} ${cart[2]}`;\n\n const sd = site.properties?.selectiveDynamics;\n\n if (sd) {\n line += ` ${sd.map((f: boolean) => (f ? \"T\" : \"F\")).join(\" \")}`;\n }\n\n lines.push(line);\n }\n\n return lines.join(\"\\n\");\n}\n","import { createLattice } from \"../lattice\";\n\nimport { fractional, cartesian } from \"../site\";\nimport { Structure } from \"../structure\";\n\n/* Parses an OPTIMADE structure data object into a Structure. /\nexport function fromOptimade(data: any): Structure {\n const lattice = createLattice([\n ...data.attributes.lattice_vectors[0],\n ...data.attributes.lattice_vectors[1],\n ...data.attributes.lattice_vectors[2],\n ]);\n\n const positions = data.attributes.cartesian_site_positions;\n const species = data.attributes.species_at_sites;\n\n const sites = positions.map((position: number[], i: number) => ({\n species: {\n symbol: species[i],\n },\n\n frac: fractional(lattice, new Float64Array(position)),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\n/* Serializes a Structure to an OPTIMADE-compatible data object. /\nexport function toOptimade(structure: Structure) {\n const m = structure.lattice.basis.data;\n\n const species_at_sites = structure.sites.map((site) => site.species.symbol);\n\n const elements = [...new Set(species_at_sites)].sort();\n\n return {\n attributes: {\n lattice_vectors: [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ],\n\n species_at_sites,\n\n cartesian_site_positions: structure.sites.map((site) =>\n Array.from(cartesian(structure.lattice, site)),\n ),\n\n dimension_types: [1, 1, 1],\n\n nsites: structure.sites.length,\n\n nelements: elements.length,\n\n elements,\n },\n };\n}\n","/\n Convert a single measurement between units.\n \n Note on floating point: conversion routes through the base unit, so each\n * call applies two roundings (`value * fromFactor / toFactor`). The result\n * can differ by 1 ulp from multiplying by a direct factor (e.g.\n * `convert(v, \"Hartree\", \"Rydberg\")` is not bit-identical to `v * 2` for all\n * doubles). Callers that need bit-exact round-trips should resolve the\n * factor once (e.g. `convert(1, from, to)`) and apply it in a tight loop\n * instead of converting per value — which is also much faster.\n \n @param value - Numeric value to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Converted value.\n /\nexport function convertMeasurement<T extends string>(\n value: number,\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number {\n const resolve = (u: string) => (aliases?.[u] ?? u) as T;\n\n const fromUnit = resolve(from);\n const toUnit = resolve(to);\n\n if (fromUnit === toUnit) return value;\n\n const valueInBase = value conversions[fromUnit];\n return valueInBase / conversions[toUnit];\n}\n\n/*\n Convert an array of measurements between units.\n \n Same floating-point caveat as convertMeasurement applies per element; in\n * addition this allocates a plain number[] and performs map lookups per\n * value, so for large typed arrays prefer resolving the factor once and\n * looping directly.\n \n @param arr - Array of numeric values to convert.\n * @param from - Source unit.\n * @param to - Target unit.\n * @param conversions - Map of unit to base conversion factor.\n * @param aliases - Optional alias map for unit names.\n * @returns Array of converted values.\n /\nexport function convertMeasurementArray<T extends string>(\n arr: number[],\n from: T,\n to: T,\n conversions: Record<T, number>,\n aliases?: Record<string, T>,\n): number[] {\n return arr.map((v) => convertMeasurement(v, from, to, conversions, aliases));\n}\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported length unit identifiers. /\nexport type LengthUnits =\n \| \"angstrom\"\n \| \"bohr\"\n \| \"nm\"\n \| \"pm\"\n \| \"cm\"\n \| \"m\"\n \| \"um\"\n \| \"fm\";\n\nconst LengthConversions: Record<LengthUnits, number> = {\n angstrom: 1,\n bohr: 0.529177,\n nm: 10,\n pm: 0.01,\n um: 1e4,\n cm: 1e8,\n m: 1e10,\n fm: 1e-5,\n};\n\nconst LengthAliases: Record<string, LengthUnits> = {\n Å: \"angstrom\",\n μm: \"um\",\n};\n\n/* Unit system for length conversions with angstrom as base. /\nexport const LengthUnitSystem = {\n conversions: LengthConversions,\n aliases: LengthAliases,\n\n convert(value: number, from: LengthUnits \| string, to: LengthUnits \| string) {\n return convertMeasurement(\n value,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: LengthUnits \| string,\n to: LengthUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as LengthUnits,\n to as LengthUnits,\n LengthConversions,\n LengthAliases,\n );\n },\n};\n","// derived from https://manual.gromacs.org/current/reference-manual/file-formats.html#gro\n\n// NOTE: GROMACS stores all lengths (coordinates and box vectors) in nm.\n// Internally matsci-parse uses Å.\n\n// Its common convention for GROMACs to use Hw or Ow for water, we dont try to fix this at-all\n// therefore cross format parsing (to a software that needs elemental indication) will probably fail.\n\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\nimport { LengthUnitSystem } from \"../units/length\";\n\nfunction pad5(str: string) {\n return str.length > 5 ? str.slice(0, 5) : str.padStart(5);\n}\n\nfunction formatCoord(x: number) {\n return x.toFixed(3).padStart(8);\n}\n\n/* Parses a GROMACS GRO string into a Structure. /\nexport function fromGRO(text: string): Structure {\n const lines = text.split(/\\r?\\n/).filter((l) => l.length > 0);\n\n let cursor = 0;\n\n const title = lines[cursor++];\n\n const timeMatch = title.match(/t=\\s([-+]?[0-9]\\.?[0-9]+)/i);\n const time = timeMatch ? Number(timeMatch[1]) : undefined;\n\n const nAtoms = Number(lines[cursor++]);\n\n if (!Number.isFinite(nAtoms)) {\n throw new Error(\"Invalid GRO atom count\");\n }\n\n type Atom = {\n symbol: string;\n cart: Float64Array;\n };\n\n const atoms: Atom[] = [];\n\n for (let i = 0; i < nAtoms; i++) {\n const line = lines[cursor++];\n\n const x = Number(line.slice(20, 28));\n const y = Number(line.slice(28, 36));\n const z = Number(line.slice(36, 44));\n\n let atomName = line.slice(10, 15).trim();\n\n let symbol = atomName.replace(/[0-9]/g, \"\");\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n\n atoms.push({\n symbol,\n cart: new Float64Array(\n LengthUnitSystem.convertArray([x, y, z], \"nm\", \"angstrom\"),\n ),\n });\n }\n\n let lattice = null;\n\n const boxLine = lines[cursor];\n\n if (boxLine) {\n const vals = boxLine.trim().split(/\\s+/).map(Number);\n\n const matrix = LengthUnitSystem.convertArray(\n [\n vals[0] ?? 0,\n vals[3] ?? 0,\n vals[4] ?? 0,\n vals[5] ?? 0,\n vals[1] ?? 0,\n vals[6] ?? 0,\n vals[7] ?? 0,\n vals[8] ?? 0,\n vals[2] ?? 0,\n ],\n \"nm\",\n \"angstrom\",\n );\n\n const hasOffDiagonal =\n matrix[1] !== 0 \|\|\n matrix[2] !== 0 \|\|\n matrix[3] !== 0 \|\|\n matrix[5] !== 0 \|\|\n matrix[6] !== 0 \|\|\n matrix[7] !== 0;\n\n lattice = hasOffDiagonal\n ? createLattice(matrix)\n : createLattice([matrix[0], matrix[4], matrix[8]]);\n }\n\n const sites: Site[] = atoms.map((atom) => ({\n species: { symbol: atom.symbol },\n frac: lattice\n ? fractional(lattice, atom.cart)\n : new Float64Array([NaN, NaN, NaN]),\n }));\n\n return {\n lattice,\n sites,\n time,\n };\n}\n\n/* Serializes a Structure to a GROMACS GRO string. /\nexport function toGRO(\n structure: Structure,\n options?: {\n title?: string;\n time?: number;\n },\n): string {\n const title =\n options?.title ??\n (options?.time !== undefined\n ? `Generated structure, t=${options.time}`\n : \"Generated by matsci-parse\");\n\n const lines: string[] = [];\n\n lines.push(title);\n lines.push(String(structure.sites.length));\n\n for (let i = 0; i < structure.sites.length; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n\n const [x, y, z] = LengthUnitSystem.convertArray(\n Array.from(cart),\n \"angstrom\",\n \"nm\",\n );\n\n lines.push(\n pad5(\"1\") +\n pad5(\"RES\") +\n pad5(site.species.symbol) +\n pad5(String(i + 1)) +\n formatCoord(x) +\n formatCoord(y) +\n formatCoord(z),\n );\n }\n\n const m = structure.lattice.basis.data;\n\n const [a, b, c] = LengthUnitSystem.convertArray(\n [m[0], m[4], m[8]],\n \"angstrom\",\n \"nm\",\n );\n\n lines.push([a, b, c].map((v) => v.toFixed(5)).join(\" \"));\n\n return lines.join(\"\\n\");\n}\n","import { fromParameters } from \"../lattice\";\nimport { createLattice } from \"../lattice\";\nimport { cartesian } from \"../site\";\nimport { fractional } from \"../site/fractional\";\nimport { Site } from \"../site/site\";\nimport { Structure } from \"../structure/structure\";\n\nconst DEFAULT_PADDING = 10.0;\n\nfunction parseCRYST1(line: string) {\n const a = Number(line.slice(6, 15));\n const b = Number(line.slice(15, 24));\n const c = Number(line.slice(24, 33));\n\n const alpha = Number(line.slice(33, 40));\n const beta = Number(line.slice(40, 47));\n const gamma = Number(line.slice(47, 54));\n\n return { a, b, c, alpha, beta, gamma };\n}\n\nfunction isCRYST1Sane(\n a: number,\n b: number,\n c: number,\n extentX: number,\n extentY: number,\n extentZ: number,\n): boolean {\n // reject degenerate or identity cells\n if (a <= 1e-3 \|\| b <= 1e-3 \|\| c <= 1e-3) return false;\n\n // reject clearly too small cells\n const margin = 1.2; // allow small packing inefficiency\n\n if (a < extentX margin) return false;\n if (b < extentY * margin) return false;\n if (c < extentZ * margin) return false;\n\n // also reject ridiculous huge identity placeholders\n if (a === 1 && b === 1 && c === 1) return false;\n\n return true;\n}\n\n/** Parses a PDB (Protein Data Bank) string into a Structure. /\nexport function fromPDB(text: string): Structure {\n const lines = text.split(/\\r?\\n/);\n\n let crystal: {\n a: number;\n b: number;\n c: number;\n alpha: number;\n beta: number;\n gamma: number;\n } \| null = null;\n\n type ParsedAtom = {\n symbol: string;\n x: number;\n y: number;\n z: number;\n };\n\n const atoms: ParsedAtom[] = [];\n\n let xmin = Infinity;\n let ymin = Infinity;\n let zmin = Infinity;\n\n let xmax = -Infinity;\n let ymax = -Infinity;\n let zmax = -Infinity;\n\n for (const line of lines) {\n if (line.startsWith(\"CRYST1\")) {\n crystal = parseCRYST1(line);\n continue;\n }\n\n if (!line.startsWith(\"ATOM \") && !line.startsWith(\"HETATM\")) {\n continue;\n }\n\n const x = Number(line.slice(30, 38));\n const y = Number(line.slice(38, 46));\n const z = Number(line.slice(46, 54));\n\n let symbol = line.slice(76, 78).trim();\n\n if (!symbol) {\n symbol = line.slice(12, 16).replace(/[0-9]/g, \"\").trim();\n symbol = symbol.charAt(0).toUpperCase() + symbol.slice(1).toLowerCase();\n }\n\n atoms.push({ symbol, x, y, z });\n\n xmin = Math.min(xmin, x);\n ymin = Math.min(ymin, y);\n zmin = Math.min(zmin, z);\n\n xmax = Math.max(xmax, x);\n ymax = Math.max(ymax, y);\n zmax = Math.max(zmax, z);\n }\n\n if (atoms.length === 0) {\n throw new Error(\"No ATOM/HETATM records found.\");\n }\n\n const extentX = xmax - xmin;\n const extentY = ymax - ymin;\n const extentZ = zmax - zmin;\n\n let lattice = createLattice([1, 0, 0, 0, 1, 0, 0, 0, 1]);\n\n let originX = xmin - DEFAULT_PADDING;\n let originY = ymin - DEFAULT_PADDING;\n let originZ = zmin - DEFAULT_PADDING;\n\n const useCrystal =\n crystal !== null &&\n isCRYST1Sane(crystal.a, crystal.b, crystal.c, extentX, extentY, extentZ);\n\n if (useCrystal) {\n lattice = fromParameters(\n crystal.a,\n crystal.b,\n crystal.c,\n crystal.alpha,\n crystal.beta,\n crystal.gamma,\n );\n\n originX = 0;\n originY = 0;\n originZ = 0;\n } else {\n const a = Math.max(extentX + 2 DEFAULT_PADDING, 1.0);\n const b = Math.max(extentY + 2 * DEFAULT_PADDING, 1.0);\n const c = Math.max(extentZ + 2 * DEFAULT_PADDING, 1.0);\n\n lattice = createLattice([a, 0, 0, 0, b, 0, 0, 0, c]);\n }\n\n const sites: Site[] = atoms.map(({ symbol, x, y, z }) => ({\n species: { symbol },\n frac: fractional(\n lattice,\n new Float64Array([x - originX, y - originY, z - originZ]),\n ),\n }));\n\n return {\n lattice,\n sites,\n };\n}\n\n/** Serializes a Structure to a PDB string. /\nexport function toPDB(\n structure: Structure,\n options?: {\n title?: string;\n },\n): string {\n const title = options?.title ?? \"Generated by matsci-parse\";\n\n const lines: string[] = [];\n\n lines.push(`HEADER ${title}`);\n\n let index = 1;\n\n for (const site of structure.sites) {\n const c = cartesian(structure.lattice, site);\n\n const symbol = site.species.symbol;\n\n lines.push(\n [\n \"ATOM \",\n index.toString().padStart(5),\n \" \",\n symbol.padEnd(4),\n \" MOL \",\n \"A\",\n \" 1 \",\n c[0].toFixed(3).padStart(8),\n c[1].toFixed(3).padStart(8),\n c[2].toFixed(3).padStart(8),\n \" 1.00\",\n \" 0.00\",\n \" \",\n symbol.padStart(2),\n ].join(\"\"),\n );\n\n index++;\n }\n\n lines.push(\"END\");\n\n return lines.join(\"\\n\");\n}\n","/\n QE ibrav → Lattice vector mapping.\n \n Implements all 29 QE ibrav values (-14 to +14, excluding 0).\n * Maps the ibrav index + celldm or A,B,C parameters to a 3x3 lattice basis.\n \n @see https://www.quantum-espresso.org/Doc/INPUT_PW.html\n /\n\nimport { createLattice } from \"../../lattice\";\nimport type { Lattice } from \"../../lattice\";\nimport { fromParameters } from \"../../lattice/create/fromParameters\";\nimport { clean } from \"../../math/numeric\";\n\nconst SQRT3 = Math.sqrt(3);\nconst SQRT2 = Math.sqrt(2);\n\n/\n Construct a Lattice from QE ibrav index and crystal parameters.\n \n Output units: Bohr. The caller must convert to Angstrom if needed.\n \n @param ibrav Bravais lattice index (-14 to +14, excluding 0)\n * @param celldm celldm(1..6): celldm(1) in Bohr, others unitless ratios/cosines\n * @param ABC Optional alternative: [A, B, C, cosAB, cosAC, cosBC] with A,B,C in Angstrom\n /\nexport function ibravToLattice(\n ibrav: number,\n celldm: number[],\n ABC?: [number, number, number, number, number, number],\n): Lattice {\n if (ibrav === 0) {\n throw new Error(\"ibrav=0 requires explicit CELL_PARAMETERS\");\n }\n\n // resolve lattice parameter a in Bohr\n let a: number;\n let b: number;\n let c: number;\n let cosab: number;\n let cosac: number;\n let cosbc: number;\n\n if (ABC) {\n // A,B,C in Angstrom → convert to Bohr\n const [Av, Bv, Cv, cosAB, cosAC, cosBC] = ABC;\n a = Av BOHR_PER_ANGSTROM;\n b = Bv * BOHR_PER_ANGSTROM;\n c = Cv * BOHR_PER_ANGSTROM;\n cosab = cosAB;\n cosac = cosAC;\n cosbc = cosBC;\n } else {\n a = celldm[0] ?? 0;\n b = a * (celldm[1] ?? 0);\n c = a * (celldm[2] ?? 0);\n\n // meaning of celldm(4..6) depends on ibrav\n // defaults set per-case below\n cosab = 0;\n cosac = 0;\n cosbc = 0;\n }\n\n const v: number[] = new Array(9);\n\n switch (ibrav) {\n case 1: {\n // Cubic P (sc): v1 = a(1,0,0), v2 = a(0,1,0), v3 = a(0,0,1)\n const pp = fromParameters(a, a, a, 90, 90, 90);\n return pp;\n }\n\n case 2: {\n // Cubic F (fcc): v1 = (a/2)(-1,0,1), v2 = (a/2)(0,1,1), v3 = (a/2)(-1,1,0)\n const h = a / 2;\n v[0] = -h; v[1] = 0; v[2] = h;\n v[3] = 0; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = h; v[8] = 0;\n break;\n }\n\n case 3: {\n // Cubic I (bcc): v1 = (a/2)(1,1,1), v2 = (a/2)(-1,1,1), v3 = (a/2)(-1,-1,1)\n const h = a / 2;\n v[0] = h; v[1] = h; v[2] = h;\n v[3] = -h; v[4] = h; v[5] = h;\n v[6] = -h; v[7] = -h; v[8] = h;\n break;\n }\n\n case -3: {\n // Cubic I (bcc), more symmetric: v1 = (a/2)(-1,1,1), v2 = (a/2)(1,-1,1), v3 = (a/2)(1,1,-1)\n const h = a / 2;\n v[0] = -h; v[1] = h; v[2] = h;\n v[3] = h; v[4] = -h; v[5] = h;\n v[6] = h; v[7] = h; v[8] = -h;\n break;\n }\n\n case 4: {\n // Hexagonal and Trigonal P: celldm(3) = c/a\n // v1 = a(1,0,0), v2 = a(-1/2, sqrt(3)/2, 0), v3 = a(0,0,c/a)\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 120);\n }\n\n case 5: {\n // Trigonal R, 3fold axis c: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n v[0] = a * tx; v[1] = -a * ty; v[2] = a * tz;\n v[3] = 0; v[4] = a * 2 * ty; v[5] = a * tz;\n v[6] = -a * tx; v[7] = -a * ty; v[8] = a * tz;\n break;\n }\n\n case -5: {\n // Trigonal R, 3fold axis <111>: celldm(4) = cos(gamma)\n const c4 = ABC ? cosbc : (celldm[3] ?? 0);\n const tx = Math.sqrt((1 - c4) / 2);\n const ty = Math.sqrt((1 - c4) / 6);\n const tz = Math.sqrt((1 + 2 * c4) / 3);\n const u = tz - 2 * SQRT2 * ty;\n const vv = tz + SQRT2 * ty;\n const ap = a / SQRT3;\n v[0] = ap * u; v[1] = ap * vv; v[2] = ap * vv;\n v[3] = ap * vv; v[4] = ap * u; v[5] = ap * vv;\n v[6] = ap * vv; v[7] = ap * vv; v[8] = ap * u;\n break;\n }\n\n case 6: {\n // Tetragonal P (st): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a, a * ca, 90, 90, 90);\n }\n\n case 7: {\n // Tetragonal I (bct): celldm(3) = c/a\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const h = a / 2;\n const hh = h * ca;\n v[0] = h; v[1] = -h; v[2] = hh;\n v[3] = h; v[4] = h; v[5] = hh;\n v[6] = -h; v[7] = -h; v[8] = hh;\n break;\n }\n\n case 8: {\n // Orthorhombic P: celldm(2) = b/a, celldm(3) = c/a\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n return fromParameters(a, a * ba, a * ca, 90, 90, 90);\n }\n\n case 9: {\n // Orthorhombic base-centered (bco): celldm(2) = b/a, celldm(3) = c/a\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case -9: {\n // Orthorhombic BC, alternate: v1 = (a/2, -b/2, 0), v2 = (a/2, b/2, 0), v3 = (0, 0, c)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = -bb / 2; v[2] = 0;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = 0; v[8] = cc;\n break;\n }\n\n case 91: {\n // Orthorhombic one-face base-centered A-type\n // v1 = (a, 0, 0), v2 = (0, b/2, -c/2), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a; v[1] = 0; v[2] = 0;\n v[3] = 0; v[4] = bb / 2; v[5] = -cc / 2;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 10: {\n // Orthorhombic face-centered\n // v1 = (a/2, 0, c/2), v2 = (a/2, b/2, 0), v3 = (0, b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = cc / 2;\n v[3] = a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = 0; v[7] = bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 11: {\n // Orthorhombic body-centered\n // v1 = (a/2, b/2, c/2), v2 = (-a/2, b/2, c/2), v3 = (-a/2, -b/2, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = cc / 2;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = cc / 2;\n v[6] = -a / 2; v[7] = -bb / 2; v[8] = cc / 2;\n break;\n }\n\n case 12: {\n // Monoclinic P, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const gamma = Math.acos(cg) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, 90, gamma);\n }\n\n case -12: {\n // Monoclinic P, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const beta = Math.acos(cb) * (180 / Math.PI);\n return fromParameters(a, a * ba, a * ca, 90, beta, 90);\n }\n\n case 13: {\n // Monoclinic base-centered, unique axis c: celldm(2) = b/a, celldm(3) = c/a, celldm(4) = cos(gamma)\n // v1 = (a/2, 0, -c/2), v2 = (bcos(gamma), bsin(gamma), 0), v3 = (a/2, 0, c/2)\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cg = ABC ? cosab : (celldm[3] ?? 0);\n const sg = Math.sqrt(Math.max(0, 1 - cg * cg));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = 0; v[2] = -cc / 2;\n v[3] = bb * cg; v[4] = bb * sg; v[5] = 0;\n v[6] = a / 2; v[7] = 0; v[8] = cc / 2;\n break;\n }\n\n case -13: {\n // Monoclinic base-centered, unique axis b: celldm(2) = b/a, celldm(3) = c/a, celldm(5) = cos(beta)\n // v1 = (a/2, b/2, 0), v2 = (-a/2, b/2, 0), v3 = (ccos(beta), 0, csin(beta))\n const ba = ABC ? b / a : (celldm[1] ?? 1);\n const ca = ABC ? c / a : (celldm[2] ?? 1);\n const cb = ABC ? cosac : (celldm[4] ?? 0);\n const sb = Math.sqrt(Math.max(0, 1 - cb * cb));\n const bb = a * ba;\n const cc = a * ca;\n v[0] = a / 2; v[1] = bb / 2; v[2] = 0;\n v[3] = -a / 2; v[4] = bb / 2; v[5] = 0;\n v[6] = cc * cb; v[7] = 0; v[8] = cc * sb;\n break;\n }\n\n case 14: {\n // Triclinic: celldm(2..6)\n // Same as fromParameters with explicit angles\n if (ABC) {\n return fromParameters(a, b, c,\n Math.acos(cosbc) * (180 / Math.PI),\n Math.acos(cosac) * (180 / Math.PI),\n Math.acos(cosab) * (180 / Math.PI),\n );\n }\n const ba = celldm[1] ?? 1;\n const ca = celldm[2] ?? 1;\n const cbc = celldm[3] ?? 0; // cos(alpha) between b and c\n const cac = celldm[4] ?? 0; // cos(beta) between a and c\n const cab = celldm[5] ?? 0; // cos(gamma) between a and b\n const bb = a * ba;\n const cc = a * ca;\n return fromParameters(a, bb, cc,\n Math.acos(cbc) * (180 / Math.PI),\n Math.acos(cac) * (180 / Math.PI),\n Math.acos(cab) * (180 / Math.PI),\n );\n }\n\n default:\n throw new Error(`Unsupported ibrav value: ${ibrav}`);\n }\n\n return createLattice(v.map(clean));\n}\n","/*\n Quantum ESPRESSO Fortran namelist parser.\n \n Parses QE-style namelists (`&NAME ... /`) from input text.\n * Supports strings, reals (including Fortran D notation),\n * logicals, integers, and array syntax `key(i) = value`.\n /\n\nexport interface QeNamelist {\n /* Namelist block name (uppercase). /\n name: string;\n /* Key → raw string value (keys stored lowercase). /\n values: Map<string, string>;\n}\n\nfunction convertFortranReal(s: string): string {\n const v = s.replace(/[dD]/g, \"e\");\n return String(Number.parseFloat(v));\n}\n\nfunction convertValue(raw: string): string {\n const trimmed = raw.trim();\n\n // quoted string\n if (\n (trimmed.startsWith(\"'\") && trimmed.endsWith(\"'\")) \|\|\n (trimmed.startsWith('\"') && trimmed.endsWith('\"'))\n ) {\n return trimmed.slice(1, -1);\n }\n\n // logical\n if (/^\\.(?:true\|false)\\.$/i.test(trimmed)) {\n return trimmed.toLowerCase() === \".true.\" ? \"true\" : \"false\";\n }\n\n // Fortran D-notation real\n if (/[dD]/.test(trimmed)) {\n return convertFortranReal(trimmed);\n }\n\n return trimmed;\n}\n\n/\n Parse a single QE namelist block from lines.\n * Returns the namelist and the index after the closing `/`.\n /\nfunction parseOne(\n lines: string[],\n start: number,\n): { namelist: QeNamelist; end: number } \| null {\n const openLine = lines[start].trim();\n\n const openMatch = openLine.match(/^&(\\w+)/i);\n if (!openMatch) return null;\n\n const name = openMatch[1].toUpperCase();\n const values = new Map<string, string>();\n\n for (let i = start + 1; i < lines.length; i++) {\n let line = lines[i];\n\n // strip inline comments\n const commentIdx = line.indexOf(\"!\");\n if (commentIdx >= 0) line = line.slice(0, commentIdx);\n\n // closing slash\n if (/^\\//.test(line.trim())) {\n return { namelist: { name, values }, end: i };\n }\n\n // key = value pairs (commas optional)\n const pairs = line.split(\",\");\n for (const pair of pairs) {\n const eqIdx = pair.indexOf(\"=\");\n if (eqIdx < 0) continue;\n\n const key = pair.slice(0, eqIdx).trim().toLowerCase();\n const raw = pair.slice(eqIdx + 1);\n\n if (!key) continue;\n\n // check for array syntax: key(i)\n const arrMatch = key.match(/^(\\w+)\$(\\d+)\$$/);\n const storeKey = arrMatch ? `${arrMatch[1]}(${arrMatch[2]})` : key;\n\n values.set(storeKey, convertValue(raw));\n }\n }\n\n // unterminated namelist\n return { namelist: { name, values }, end: lines.length };\n}\n\n/\n Parse all QE namelists from input text.\n * Returns namelists in order of appearance.\n /\nexport function parseQeNamelist(text: string): QeNamelist[] {\n const lines = text.split(\"\\n\");\n const result: QeNamelist[] = [];\n\n for (let i = 0; i < lines.length; i++) {\n if (/^\\s&\\w+/.test(lines[i])) {\n const parsed = parseOne(lines, i);\n if (parsed) {\n result.push(parsed.namelist);\n i = parsed.end;\n }\n }\n }\n\n return result;\n}\n\n/** Find a namelist block by name. /\nfunction findBlock(\n namelists: QeNamelist[],\n block: string,\n): QeNamelist \| undefined {\n const upper = block.toUpperCase();\n return namelists.find((n) => n.name === upper);\n}\n\n/* Get a raw string value from a namelist block. /\nexport function getString(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): string \| undefined {\n return findBlock(namelists, block)?.values.get(key.toLowerCase());\n}\n\n/* Get a numeric value from a namelist block. /\nexport function getNumber(\n namelists: QeNamelist[],\n block: string,\n key: string,\n): number \| undefined {\n const raw = getString(namelists, block, key);\n if (raw === undefined) return undefined;\n const n = Number.parseFloat(raw);\n return Number.isNaN(n) ? undefined : n;\n}\n\n/* Get an array value (e.g. celldm(1)..celldm(6)) from a namelist block. /\nexport function getArray(\n namelists: QeNamelist[],\n block: string,\n key: string,\n size: number,\n): number[] {\n const lower = key.toLowerCase();\n const result: number[] = [];\n for (let i = 1; i <= size; i++) {\n const raw = getString(namelists, block, `${lower}(${i})`);\n if (raw !== undefined) {\n result.push(Number.parseFloat(raw));\n } else {\n result.push(0);\n }\n }\n return result;\n}\n","import { createLattice } from \"../../lattice/lattice\";\nimport { kspacingToGrid } from \"../../lattice/kspacingToGrid\";\nimport { ibravToLattice } from \"./ibrav\";\nimport { fractional } from \"../../site\";\nimport { getElement } from \"../../data/periodictable/atomicData\";\nimport type { Site } from \"../../site/site\";\nimport type { Structure } from \"../../structure/structure\";\nimport { parseQeNamelist, getNumber, getString, getArray } from \"./namelist\";\nimport type {\n AtomicSpeciesEntry,\n AtomicPositionEntry,\n CellParameterEntry,\n KPointsCard,\n} from \"./schema/cards\";\nimport type { QeControlOptions } from \"./schema/control\";\nimport type { QeSystemOptions } from \"./schema/system\";\nimport type { QeElectronsOptions } from \"./schema/electrons\";\n\nconst BOHR_TO_ANGSTROM = 0.529177;\n\ntype AtomCoordMode = \"crystal\" \| \"angstrom\" \| \"bohr\" \| \"alat\";\n\n// ──────────────────────────────────────────────────────────────────────\n// Options — composed from schema types\n// ──────────────────────────────────────────────────────────────────────\n\n/* User-facing options for {@link toPW}. Composed from schema types. /\nexport interface QEOptions {\n control?: QeControlOptions;\n system?: QeSystemOptions;\n electrons?: QeElectronsOptions;\n kpoints?:\n \| { grid: [number, number, number]; shift?: [number, number, number] }\n \| { kspacing: number };\n pseudo?: { pseudos?: Record<string, string> };\n}\n\nconst QE_DEFAULTS: Required<\n Pick<QEOptions, \"control\" \| \"system\" \| \"electrons\" \| \"kpoints\" \| \"pseudo\">\n> = {\n control: {\n title: \"Generated by matsci-parse\",\n calculation: \"scf\",\n pseudo_dir: \"./\",\n },\n system: {\n ecutwfc: 30,\n },\n electrons: {\n conv_thr: 1e-6,\n },\n kpoints: { kspacing: 0.22 },\n pseudo: { pseudos: {} },\n};\n\n// ──────────────────────────────────────────────────────────────────────\n// fromPW — unchanged\n// ──────────────────────────────────────────────────────────────────────\n\n/* Parses a Quantum ESPRESSO PW input string into a Structure. /\nexport function fromPW(text: string): Structure {\n const namelists = parseQeNamelist(text);\n const lines = text.split(\"\\n\");\n\n // --- extract &SYSTEM parameters ---\n const ibrav = getNumber(namelists, \"SYSTEM\", \"ibrav\") ?? 0;\n const nat = getNumber(namelists, \"SYSTEM\", \"nat\");\n const celldm = getArray(namelists, \"SYSTEM\", \"celldm\", 6);\n\n // --- build lattice ---\n let lattice: ReturnType<typeof createLattice>;\n\n if (ibrav !== 0) {\n // ibravToLattice returns lattice vectors in Bohr → convert to angstrom\n const bohr = ibravToLattice(ibrav, celldm);\n const m = bohr.basis.data;\n lattice = createLattice([\n m[0] BOHR_TO_ANGSTROM,\n m[1] * BOHR_TO_ANGSTROM,\n m[2] * BOHR_TO_ANGSTROM,\n m[3] * BOHR_TO_ANGSTROM,\n m[4] * BOHR_TO_ANGSTROM,\n m[5] * BOHR_TO_ANGSTROM,\n m[6] * BOHR_TO_ANGSTROM,\n m[7] * BOHR_TO_ANGSTROM,\n m[8] * BOHR_TO_ANGSTROM,\n ]);\n } else {\n // ibrav=0: lattice must come from CELL_PARAMETERS block\n const { lattice: cellLattice, units: cellUnits } =\n parseCellParameters(lines);\n\n if (cellUnits === \"alat\") {\n if (celldm[0] === 0) {\n throw new Error(\"CELL_PARAMETERS alat requires celldm(1) in &SYSTEM\");\n }\n // lattice vectors are in units of celldm(1) Bohr → convert to angstrom\n const factor = celldm[0] / BOHR_TO_ANGSTROM;\n const m = cellLattice.basis.data;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else if (cellUnits === \"bohr\") {\n // lattice vectors in Bohr → convert to angstrom\n const m = cellLattice.basis.data;\n const factor = 1 / BOHR_TO_ANGSTROM;\n lattice = createLattice([\n m[0] * factor,\n m[1] * factor,\n m[2] * factor,\n m[3] * factor,\n m[4] * factor,\n m[5] * factor,\n m[6] * factor,\n m[7] * factor,\n m[8] * factor,\n ]);\n } else {\n // angstrom — use directly\n lattice = cellLattice;\n }\n }\n\n // --- parse atomic positions ---\n const {\n lines: atomLines,\n units,\n selectiveDynamics,\n } = parseAtomicPositions(lines);\n\n if (atomLines.length === 0) {\n throw new Error(\"ATOMIC_POSITIONS block not found\");\n }\n\n if (nat !== undefined && atomLines.length !== nat) {\n throw new Error(\n `Expected ${nat} atoms (from &SYSTEM nat), got ${atomLines.length}`,\n );\n }\n\n const sites: Site[] = [];\n\n for (const line of atomLines) {\n const parts = line.split(/\\s+/);\n const symbol = parts[0];\n const x = +parts[1];\n const y = +parts[2];\n const z = +parts[3];\n\n let frac: Float64Array;\n\n switch (units) {\n case \"crystal\":\n frac = new Float64Array([x, y, z]);\n break;\n\n case \"angstrom\":\n frac = fractional(lattice, new Float64Array([x, y, z]));\n break;\n\n case \"bohr\": {\n // Bohr → angstrom → fractional\n const angstrom = new Float64Array([\n x * BOHR_TO_ANGSTROM,\n y * BOHR_TO_ANGSTROM,\n z * BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n\n case \"alat\": {\n // alat = celldm(1) Bohr → Bohr → angstrom → fractional\n if (celldm[0] === 0) {\n throw new Error(\n \"ATOMIC_POSITIONS alat requires celldm(1) in &SYSTEM\",\n );\n }\n const bohr = new Float64Array([\n x * celldm[0],\n y * celldm[0],\n z * celldm[0],\n ]);\n const angstrom = new Float64Array([\n bohr[0] / BOHR_TO_ANGSTROM,\n bohr[1] / BOHR_TO_ANGSTROM,\n bohr[2] / BOHR_TO_ANGSTROM,\n ]);\n frac = fractional(lattice, angstrom);\n break;\n }\n }\n\n const site: Site = { species: { symbol }, frac };\n\n if (selectiveDynamics && parts.length >= 7) {\n const ifPos = [+parts[4], +parts[5], +parts[6]];\n (site.properties ??= {}).ifPos = ifPos;\n }\n\n sites.push(site);\n }\n\n return {\n lattice,\n sites,\n ...(selectiveDynamics ? { selectiveDynamics: true } : {}),\n };\n}\n\n// ---------- internal parsing helpers ----------\n\ninterface CellParamsResult {\n lattice: ReturnType<typeof createLattice>;\n units: string;\n}\n\nfunction parseCellParameters(lines: string[]): CellParamsResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^CELL_PARAMETERS/i.test(line)) {\n const unitMatch = line.match(\n /^CELL_PARAMETERS\\s(?:\\{\|\$)?(\\w+)(?:\\}\|\$)?/i,\n );\n const units = unitMatch?.[1]?.toLowerCase() ?? \"angstrom\";\n\n const rows: number[][] = [];\n for (let j = 1; j <= 3; j++) {\n if (i + j >= lines.length) {\n throw new Error(\"Incomplete CELL_PARAMETERS block\");\n }\n rows.push(lines[i + j].trim().split(/\\s+/).map(Number));\n }\n\n return {\n lattice: createLattice([...rows[0], ...rows[1], ...rows[2]]),\n units,\n };\n }\n }\n\n throw new Error(\"CELL_PARAMETERS block not found\");\n}\n\ninterface AtomBlockResult {\n lines: string[];\n units: AtomCoordMode;\n selectiveDynamics: boolean;\n}\n\nfunction parseAtomicPositions(lines: string[]): AtomBlockResult {\n for (let i = 0; i < lines.length; i++) {\n const line = lines[i].trim();\n\n if (/^ATOMIC_POSITIONS/i.test(line)) {\n const unitMatch = line.match(\n /^ATOMIC_POSITIONS\\s(?:\\{\|\$)?(\\w+)(?:\\}\|\$)?/i,\n );\n const units = (unitMatch?.[1]?.toLowerCase() ??\n \"angstrom\") as AtomCoordMode;\n\n const atomLines: string[] = [];\n\n // check for \"Selective dynamics\" on the NEXT line\n let selectiveDynamics = false;\n let j = i + 1;\n if (j < lines.length && /^selective\\s+dynamics/i.test(lines[j].trim())) {\n selectiveDynamics = true;\n j++;\n }\n\n for (; j < lines.length; j++) {\n const l = lines[j].trim();\n if (!l) break;\n\n const parts = l.split(/\\s+/);\n if (\n parts.length < 4 \|\|\n !/^[A-Za-z]/.test(parts[0]) \|\|\n parts.slice(1, 4).some((x) => Number.isNaN(+x))\n ) {\n break;\n }\n\n atomLines.push(l);\n }\n\n return { lines: atomLines, units, selectiveDynamics };\n }\n }\n\n return { lines: [], units: \"angstrom\", selectiveDynamics: false };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// toPW — data-driven\n// ──────────────────────────────────────────────────────────────────────\n\nconst RESERVED: Record<string, string[]> = {\n CONTROL: [\"title\"],\n};\n\n/** Serializes a Structure to a Quantum ESPRESSO PW input string. /\nexport function toPW(structure: Structure, options?: QEOptions): string {\n const ctrl = { ...QE_DEFAULTS.control, ...options?.control };\n const sys = { ...QE_DEFAULTS.system, ...options?.system };\n const { nat: _nat, ntyp: _ntyp, ibrav: _ibrav, ...sysOpts } = sys;\n const elec = { ...QE_DEFAULTS.electrons, ...options?.electrons };\n\n // --- derive card data from Structure ---\n const speciesOrder = collectSpecies(structure.sites);\n const species = buildAtomicSpecies(speciesOrder, options?.pseudo?.pseudos);\n const positions = buildAtomicPositions(structure);\n const cell = buildCellParameters(structure.lattice);\n const kpoints = buildKPoints(structure, options?.kpoints);\n\n // --- serialize ---\n const lines: string[] = [];\n\n lines.push(`title = '${ctrl.title}'`);\n lines.push(\"\");\n writeNamelist(lines, \"CONTROL\", { ...ctrl, title: undefined });\n lines.push(\"\");\n writeNamelist(lines, \"SYSTEM\", {\n ...sysOpts,\n nat: structure.sites.length,\n ntyp: speciesOrder.length,\n ibrav: 0,\n });\n lines.push(\"\");\n writeNamelist(lines, \"ELECTRONS\", elec);\n lines.push(\"\");\n\n lines.push(...serializeAtomicSpecies(species));\n lines.push(\"\");\n lines.push(...serializeKPoints(kpoints));\n lines.push(\"\");\n lines.push(...serializeCellParameters(cell));\n lines.push(\"\");\n lines.push(\n ...serializeAtomicPositions(positions, structure.selectiveDynamics),\n );\n\n return lines.join(\"\\n\");\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card builders — Structure + options → typed card data\n// ──────────────────────────────────────────────────────────────────────\n\n/* Collect unique species in first-appearance order. /\nfunction collectSpecies(sites: Site[]): string[] {\n const seen = new Set<string>();\n const order: string[] = [];\n for (const site of sites) {\n const sym = site.species.symbol;\n if (!seen.has(sym)) {\n seen.add(sym);\n order.push(sym);\n }\n }\n return order;\n}\n\n/* Build ATOMIC_SPECIES rows from species order + pseudopotential map. /\nfunction buildAtomicSpecies(\n speciesOrder: string[],\n pseudos?: Record<string, string>,\n): AtomicSpeciesEntry[] {\n return speciesOrder.map((symbol) => {\n const el = getElement(symbol);\n return {\n symbol,\n mass: el?.mass ?? 0,\n pseudo: pseudos?.[symbol] ?? `${symbol}.UPF`,\n };\n });\n}\n\n/* Build ATOMIC_POSITIONS rows from Structure sites. /\nfunction buildAtomicPositions(structure: Structure): AtomicPositionEntry[] {\n // group sites by species in first-appearance order\n const grouped = new Map<string, Site[]>();\n for (const site of structure.sites) {\n const sym = site.species.symbol;\n const group = grouped.get(sym);\n if (group) {\n group.push(site);\n } else {\n grouped.set(sym, [site]);\n }\n }\n\n const speciesOrder = collectSpecies(structure.sites);\n const entries: AtomicPositionEntry[] = [];\n\n for (const sym of speciesOrder) {\n const group = grouped.get(sym) ?? [];\n for (const site of group) {\n const entry: AtomicPositionEntry = {\n symbol: sym,\n x: site.frac[0],\n y: site.frac[1],\n z: site.frac[2],\n };\n if (site.properties?.ifPos) {\n entry.ifPos = [\n site.properties.ifPos[0],\n site.properties.ifPos[1],\n site.properties.ifPos[2],\n ];\n }\n entries.push(entry);\n }\n }\n\n return entries;\n}\n\n/* Build CELL_PARAMETERS rows from Lattice. /\nfunction buildCellParameters(\n lattice: Structure[\"lattice\"],\n): CellParameterEntry[] {\n const m = lattice.basis.data;\n return [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ];\n}\n\n/* Build K_POINTS card from options (with kspacing default). /\nfunction buildKPoints(\n structure: Structure,\n kpoints?: QEOptions[\"kpoints\"],\n): KPointsCard {\n if (kpoints) {\n if (\"grid\" in kpoints) {\n return {\n mode: \"automatic\",\n grid: kpoints.grid,\n shift: kpoints.shift ?? [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, kpoints.kspacing),\n shift: [0, 0, 0],\n };\n }\n return {\n mode: \"automatic\",\n grid: kspacingToGrid(structure.lattice, QE_DEFAULTS.kpoints.kspacing),\n shift: [0, 0, 0],\n };\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Card serializers — typed card data → string lines\n// ──────────────────────────────────────────────────────────────────────\n\nfunction serializeAtomicSpecies(entries: AtomicSpeciesEntry[]): string[] {\n const lines = [\"ATOMIC_SPECIES\"];\n for (const e of entries) {\n lines.push(`${e.symbol} ${e.mass} ${e.pseudo}`);\n }\n return lines;\n}\n\nfunction serializeKPoints(card: KPointsCard): string[] {\n switch (card.mode) {\n case \"gamma\":\n return [\"K_POINTS gamma\"];\n case \"automatic\":\n return [\n \"K_POINTS automatic\",\n `${card.grid[0]} ${card.grid[1]} ${card.grid[2]} ${card.shift[0]} ${card.shift[1]} ${card.shift[2]}`,\n ];\n default:\n // list / bands / covering — not used by toPW but handled for completeness\n throw new Error(`K_POINTS mode '${card.mode}' not yet supported in toPW`);\n }\n}\n\nfunction serializeCellParameters(\n entries: CellParameterEntry[],\n unit: \"angstrom\" \| \"bohr\" \| \"alat\" = \"angstrom\",\n): string[] {\n const lines = [`CELL_PARAMETERS ${unit}`];\n for (const [a, b, c] of entries) {\n lines.push(`${a} ${b} ${c}`);\n }\n return lines;\n}\n\nfunction serializeAtomicPositions(\n entries: AtomicPositionEntry[],\n selectiveDynamics?: boolean,\n unit: \"crystal\" \| \"angstrom\" \| \"bohr\" \| \"alat\" = \"crystal\",\n): string[] {\n const lines = [`ATOMIC_POSITIONS ${unit}`];\n if (selectiveDynamics) {\n lines.push(\"Selective dynamics\");\n }\n for (const e of entries) {\n let suffix = \"\";\n if (e.ifPos) {\n suffix = ` ${e.ifPos[0]} ${e.ifPos[1]} ${e.ifPos[2]}`;\n }\n lines.push(`${e.symbol} ${e.x} ${e.y} ${e.z}${suffix}`);\n }\n return lines;\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Namelist serializer — generic key → value\n// ──────────────────────────────────────────────────────────────────────\n\nfunction writeNamelist(\n lines: string[],\n name: string,\n params: Record<string, unknown>,\n): void {\n const reserved = new Set(RESERVED[name] ?? []);\n const entries = Object.entries(params).filter(\n ([k, v]) => !reserved.has(k) && v !== undefined,\n );\n if (entries.length === 0) {\n lines.push(`&${name}`);\n lines.push(\"/\");\n return;\n }\n lines.push(`&${name}`);\n for (const [key, value] of entries) {\n if (typeof value === \"string\") {\n lines.push(` ${key} = '${value}'`);\n } else if (typeof value === \"boolean\") {\n lines.push(` ${key} = .${value ? \"TRUE\" : \"FALSE\"}.`);\n } else if (typeof value === \"number\" && !Number.isFinite(value)) {\n continue;\n } else {\n lines.push(` ${key} = ${value}`);\n }\n }\n lines.push(\"/\");\n}\n","import type {\n KGrid,\n KPath,\n KPointSet,\n KPoints,\n Vec3,\n} from \"../../kpoints/kpoints\";\nimport type { KPointsBands, KPointsCard, KPointsList, Kpt } from \"../pw/schema/cards\";\n\nconst K_POINTS_HEADER = /^K_POINTS(?:\\s+\\{?\$?(\\w+)\$?\\}?)?/i;\nconst NEXT_CARD =\n /^(?:ATOMIC_SPECIES\|ATOMIC_POSITIONS\|CELL_PARAMETERS\|K_POINTS\|ADDITIONAL_K_POINTS\|OCCUPATIONS\|CONSTRAINTS\|ATOMIC_VELOCITIES\|ATOMIC_FORCES\|HUBBARD\|SOLVENTS)\\b/i;\n\nfunction stripComment(line: string): string {\n let cut = line.length;\n const bang = line.indexOf(\"!\");\n const hash = line.indexOf(\"#\");\n if (bang !== -1) cut = Math.min(cut, bang);\n if (hash !== -1) cut = Math.min(cut, hash);\n return line.slice(0, cut);\n}\n\nfunction toNumbers(line: string): number[] {\n return stripComment(line)\n .split(/\\s+/)\n .filter((t) => t !== \"\")\n .map(Number);\n}\n\nfunction parseKpt(line: string): Kpt {\n const n = toNumbers(line);\n if (n.length < 4) {\n throw new Error(`Invalid K_POINTS line: ${line}`);\n }\n return { x: n[0], y: n[1], z: n[2], w: n[3] };\n}\n\nfunction parsePointList(rest: string[]): Kpt[] {\n const count = Number.parseInt(rest[0] ?? \"\", 10);\n if (Number.isNaN(count)) {\n throw new Error(\"K_POINTS list requires a point count\");\n }\n const pointLines = rest.slice(1, 1 + count);\n if (pointLines.length !== count) {\n throw new Error(`Expected ${count} k-points, got ${pointLines.length}`);\n }\n return pointLines.map(parseKpt);\n}\n\n/* Extract the K_POINTS card block from a pw.x input. /\nfunction extractKPointsBlock(text: string): string[] {\n const lines = text.split(\"\\n\");\n let start = -1;\n\n for (let i = 0; i < lines.length; i++) {\n if (K_POINTS_HEADER.test(lines[i].trim())) {\n start = i;\n break;\n }\n }\n\n if (start === -1) {\n throw new Error(\"K_POINTS card not found\");\n }\n\n const block = [lines[start].trim()];\n\n for (let i = start + 1; i < lines.length; i++) {\n const l = lines[i].trim();\n if (l === \"\" \|\| NEXT_CARD.test(l)) break;\n block.push(l);\n }\n\n return block;\n}\n\n/* Parse the K_POINTS card of a Quantum ESPRESSO pw.x input into typed card data. /\nexport function fromPWKPoints(text: string): KPointsCard {\n const block = extractKPointsBlock(text);\n const modeMatch = block[0].match(K_POINTS_HEADER);\n const mode = (modeMatch?.[1]?.toLowerCase() ??\n \"automatic\") as KPointsCard[\"mode\"];\n const rest = block.slice(1);\n\n switch (mode) {\n case \"automatic\": {\n const n = toNumbers(rest[0] ?? \"\");\n if (n.length < 6) {\n throw new Error(\"K_POINTS automatic requires 6 numbers\");\n }\n return {\n mode,\n grid: [n[0], n[1], n[2]],\n shift: [n[3], n[4], n[5]],\n };\n }\n case \"gamma\":\n return { mode };\n case \"crystal\":\n case \"tpiba\":\n return { mode, points: parsePointList(rest) };\n case \"crystal_b\":\n case \"tpiba_b\": {\n const nks = Number.parseInt(rest[0] ?? \"\", 10);\n if (Number.isNaN(nks)) {\n throw new Error(\"K_POINTS band path requires nks\");\n }\n const pointLines = rest.slice(1, 1 + nks);\n if (pointLines.length !== nks) {\n throw new Error(\n `Expected ${nks} k-points, got ${pointLines.length}`,\n );\n }\n return { mode, nks, points: pointLines.map(parseKpt) };\n }\n case \"crystal_c\":\n case \"tpiba_c\":\n return { mode, points: parsePointList(rest) };\n default:\n throw new Error(`Unsupported K_POINTS mode '${mode}'`);\n }\n}\n\nfunction serializeKpt(k: Kpt): string {\n return `${k.x} ${k.y} ${k.z} ${k.w}`;\n}\n\nfunction serializeList(card: {\n mode: \"crystal\" \| \"tpiba\" \| \"crystal_c\" \| \"tpiba_c\";\n points: Kpt[];\n}): string {\n return [\n `K_POINTS ${card.mode}`,\n String(card.points.length),\n ...card.points.map(serializeKpt),\n ].join(\"\\n\");\n}\n\n/* Serialize K_POINTS card data back to a Quantum ESPRESSO pw.x card. /\nexport function toPWKPoints(card: KPointsCard): string {\n switch (card.mode) {\n case \"gamma\":\n return \"K_POINTS gamma\";\n case \"automatic\":\n return `K_POINTS automatic\\n${card.grid.join(\" \")} ${card.shift.join(\" \")}`;\n case \"crystal\":\n case \"tpiba\":\n return serializeList(card);\n case \"crystal_b\":\n case \"tpiba_b\":\n return [\n `K_POINTS ${card.mode}`,\n String(card.nks),\n ...card.points.map(serializeKpt),\n ].join(\"\\n\");\n case \"crystal_c\":\n case \"tpiba_c\":\n return serializeList(card);\n }\n}\n\n// ──────────────────────────────────────────────────────────────────────\n// Canonical k-point conversions\n// ──────────────────────────────────────────────────────────────────────\n\n/* Default number of k-points interpolated per band-path segment. /\nconst DEFAULT_POINTS_PER_SEGMENT = 40;\n\nfunction pointListToKPointSet(\n mode: \"crystal\" \| \"tpiba\" \| \"crystal_c\" \| \"tpiba_c\",\n points: readonly Kpt[],\n): KPointSet {\n const reciprocal =\n mode === \"crystal\" \|\| mode === \"crystal_c\" ? \"reciprocal\" : \"cartesian\";\n return {\n kind: \"points\",\n points: points.map((k) => ({ coordinate: [k.x, k.y, k.z] as const })),\n weights: points.map((k) => k.w),\n coordinateSystem: reciprocal,\n };\n}\n\nfunction pathFromBandPoints(points: readonly Kpt[]): KPath {\n if (points.length < 2) {\n throw new Error(\"K_POINTS band path requires at least two points\");\n }\n const names = new Map<string, string>();\n const named: Record<string, Vec3> = {};\n const nameFor = (k: Kpt): string => {\n const key = [k.x, k.y, k.z].join(\" \");\n let name = names.get(key);\n if (name === undefined) {\n name = `k${names.size + 1}`;\n names.set(key, name);\n named[name] = [k.x, k.y, k.z];\n }\n return name;\n };\n const segments: [string, string][] = [];\n for (let i = 0; i < points.length - 1; i++) {\n segments.push([nameFor(points[i]), nameFor(points[i + 1])]);\n }\n\n // Extract density: the weight of each vertex (except the last) is the\n // number of intermediate k-points on the segment to the next vertex.\n // If all segment weights are equal, set KPath.density.\n const segmentWeights = points.slice(0, -1).map((k) => k.w);\n const density =\n segmentWeights.length > 0 &&\n segmentWeights.every((w) => w === segmentWeights[0])\n ? segmentWeights[0]\n : undefined;\n\n return { kind: \"path\", points: named, segments, density };\n}\n\n/\n Read the K_POINTS card of a Quantum ESPRESSO pw.x input and convert it to\n * the canonical k-point representation.\n \n The pw.x card may appear on its own or embedded in a full pw.in file.\n \n - automatic grids map to {@link KGrid} (mesh + origin, origin being the shift)\n * - crystal / crystal_c and tpiba / tpiba_c lists map to {@link KPointSet}\n * - crystal_b band paths map to {@link KPath} (tpiba_b needs a lattice and\n * is not supported)\n /\nexport function kpointsFromPW(text: string): KPoints {\n const card = fromPWKPoints(text);\n\n switch (card.mode) {\n case \"automatic\":\n return {\n kind: \"grid\",\n mesh: card.grid,\n origin: card.shift,\n scheme: \"gamma-centered\",\n };\n case \"gamma\":\n return {\n kind: \"grid\",\n mesh: [1, 1, 1],\n origin: [0, 0, 0],\n scheme: \"gamma-centered\",\n };\n case \"crystal\":\n case \"tpiba\":\n case \"crystal_c\":\n case \"tpiba_c\":\n return pointListToKPointSet(card.mode, card.points);\n case \"crystal_b\":\n return pathFromBandPoints(card.points);\n case \"tpiba_b\":\n throw new Error(\n \"tpiba_b band paths are expressed in 2pi/alat units; converting them requires a lattice\",\n );\n }\n}\n\nfunction pathToBandCard(\n path: KPath,\n pointsPerSegment: number,\n): KPointsBands {\n const vertices: Kpt[] = [];\n // Build the vertex list in segment order (shared endpoints collapse naturally)\n for (const [start, stop] of path.segments) {\n const s = path.points[start];\n if (!s) {\n throw new Error(`KPath references unknown point '${start}'`);\n }\n vertices.push({ x: s[0], y: s[1], z: s[2], w: pointsPerSegment });\n }\n const last = path.segments[path.segments.length - 1];\n if (last) {\n const end = path.points[last[1]];\n if (!end) {\n throw new Error(`KPath references unknown point '${last[1]}'`);\n }\n // Last vertex weight is ignored by pw.x; write 1 by convention.\n vertices.push({ x: end[0], y: end[1], z: end[2], w: 1 });\n }\n return { mode: \"crystal_b\", nks: vertices.length, points: vertices };\n}\n\nfunction kPointSetToListCard(set: KPointSet): KPointsList {\n const cartesian = set.coordinateSystem === \"cartesian\";\n return {\n mode: cartesian ? \"tpiba\" : \"crystal\",\n points: set.points.map((p, i) => ({\n x: p.coordinate[0],\n y: p.coordinate[1],\n z: p.coordinate[2],\n w: set.weights?.[i] ?? 1,\n })),\n };\n}\n\n/*\n Serialize canonical k-point data as a K_POINTS card block, ready to be\n * embedded in a Quantum ESPRESSO pw.x input file.\n \n - grids are written in automatic (Monkhorst-Pack) mode\n * - k-point sets are written as crystal (reciprocal) or tpiba (2pi/alat)\n lists, depending on their coordinate system\n * - paths are written as crystal_b band paths; `pointsPerSegment` (default\n * 40) sets the number of k-points interpolated along each segment.\n * When `pointsPerSegment` is omitted, the path's own `density` is used\n * if set, otherwise the default.\n * High-symmetry point names are written as inline comments.\n /\nexport function kpointsToPW(\n data: KPoints,\n pointsPerSegment?: number,\n): string {\n switch (data.kind) {\n case \"grid\":\n return toPWKPoints({\n mode: \"automatic\",\n grid: [...data.mesh],\n shift: [...data.origin],\n });\n case \"path\": {\n const density =\n pointsPerSegment !== undefined\n ? Math.max(1, Math.round(pointsPerSegment))\n : data.density !== undefined\n ? Math.max(1, Math.round(data.density))\n : DEFAULT_POINTS_PER_SEGMENT;\n return pathWithComments(data, density);\n }\n case \"points\":\n return toPWKPoints(kPointSetToListCard(data));\n }\n}\n\n/\n Serialize a KPath as a crystal_b card with high-symmetry point name comments.\n /\nfunction pathWithComments(path: KPath, density: number): string {\n // Build the vertex list in segment order (shared endpoints collapse naturally)\n const vertices: { x: number; y: number; z: number; label: string; w: number }[] = [];\n const seen = new Set<string>();\n for (let si = 0; si < path.segments.length; si++) {\n const [start, stop] = path.segments[si];\n const s = path.points[start];\n if (!s) {\n throw new Error(`KPath references unknown point '${start}'`);\n }\n const sKey = start;\n if (!seen.has(sKey)) {\n seen.add(sKey);\n vertices.push({ x: s[0], y: s[1], z: s[2], label: start, w: density });\n }\n }\n const last = path.segments[path.segments.length - 1];\n if (last) {\n const end = path.points[last[1]];\n if (!end) {\n throw new Error(`KPath references unknown point '${last[1]}'`);\n }\n // Last vertex weight is ignored by pw.x; write 1 by convention.\n vertices.push({ x: end[0], y: end[1], z: end[2], label: last[1], w: 1 });\n }\n\n const lines = [`K_POINTS crystal_b`, String(vertices.length)];\n for (const v of vertices) {\n lines.push(`${v.x} ${v.y} ${v.z} ${v.w} ! ${v.label}`);\n }\n return lines.join(\"\\n\");\n}\n","import type {\n GridShape,\n Vec3,\n KGrid,\n KPath,\n KPoint,\n KPointSet,\n KPoints,\n} from \"../../kpoints/kpoints\";\nimport { LineReader } from \"../helpers\";\n\n/* Comment line written for automatic-mesh output. /\nconst GRID_COMMENT = \"Automatic mesh\";\n/* Comment line written for explicit-list output. /\nconst LIST_COMMENT = \"K-points list\";\n\n/\n Parse a VASP KPOINTS file.\n \n Automatic subdivision meshes (line 2 is \"0\") become a {@link KGrid}; explicit\n * k-point lists (line 2 is a positive count) become a {@link KPointSet}; line\n * modes (line 2 is a count with a \"Line-mode\" scheme, or a negative count)\n * become a {@link KPath}. The deprecated fully-automatic mode errors out.\n /\nexport function fromKPOINTS(text: string): KPoints {\n const r = new LineReader(text);\n\n // The first line is a free-form comment. Skip any leading blank lines,\n // though there should not be any.\n let line = r.next();\n while (line !== null && line.trim() === \"\") {\n line = r.next();\n }\n if (line === null) {\n throw new Error(\"KPOINTS file is too short\");\n }\n\n const mode = r.nextTrimmed();\n const modeNumber = Number(mode);\n if (mode === \"0\") {\n return parseAutomaticMesh(r);\n }\n if (Number.isInteger(modeNumber)) {\n const scheme = r.nextTrimmed();\n // A negative count is the legacy line-mode marker; a \"Line-mode\" scheme\n // line marks the current one.\n if (scheme.toLowerCase().startsWith(\"l\") \|\| modeNumber < 0) {\n return parseLineMode(r, scheme, modeNumber < 0, Math.abs(modeNumber));\n }\n return parseExplicitList(r, scheme, modeNumber);\n }\n throw new Error(`Unsupported KPOINTS mode '${mode}'`);\n}\n\n/* Parse an automatic subdivision (mesh) card. /\nfunction parseAutomaticMesh(r: LineReader): KGrid {\n const scheme = r.nextTrimmed();\n const first = scheme.toLowerCase();\n if (first.startsWith(\"a\")) {\n throw new Error(\"KPOINTS fully-automatic mode is not yet supported\");\n }\n const monkhorstPack = first.startsWith(\"m\");\n\n const mesh = parseVec3(r.nextTrimmed(), \"mesh\");\n\n // The shift line is optional and defaults to no shift.\n const shiftLine = r.next();\n const shift: Vec3 =\n shiftLine === null \|\| shiftLine.trim() === \"\"\n ? [0, 0, 0]\n : parseVec3(shiftLine.trim(), \"shift\");\n\n return {\n kind: \"grid\",\n mesh,\n origin: monkhorstPack ? monkhorstOrigin(mesh, shift) : shift,\n scheme: monkhorstPack ? \"monkhorst-pack\" : \"gamma-centered\",\n };\n}\n\n/* Parse an explicit k-point list. /\nfunction parseExplicitList(\n r: LineReader,\n scheme: string,\n count: number,\n): KPointSet {\n const coordinateSystem = parseCoordinateSystem(scheme);\n\n const points: KPoint[] = [];\n const weights: number[] = [];\n for (let i = 0; i < count; i++) {\n const { coordinate, weight } = parsePointLine(r.nextTrimmed());\n points.push({ coordinate });\n weights.push(weight);\n }\n\n return { kind: \"points\", points, weights, coordinateSystem };\n}\n\n/\n Parse a line-mode band path. `legacyScheme` marks files where the line after\n * the (negative) count is already the coordinate system line.\n \n Coordinates are stored in the canonical fractional reciprocal form; Cartesian\n * input cannot be converted without the lattice and is rejected.\n /\nfunction parseLineMode(\n r: LineReader,\n scheme: string,\n legacyScheme: boolean,\n pointsPerLine: number,\n): KPath {\n const coordinateSystem = parseCoordinateSystem(\n legacyScheme ? scheme : r.nextTrimmed(),\n );\n if (coordinateSystem === \"cartesian\") {\n throw new Error(\n \"KPOINTS Cartesian line-mode is not yet supported\",\n );\n }\n\n // Group the remaining lines into blank-line-separated blocks, each block\n // holding the points of one or more segments (two lines per segment).\n const blocks: string[][] = [];\n let current: string[] = [];\n let line: string \| null;\n while ((line = r.next()) !== null) {\n const trimmed = line.trim();\n if (trimmed === \"\") {\n if (current.length > 0) {\n blocks.push(current);\n current = [];\n }\n } else {\n current.push(trimmed);\n }\n }\n if (current.length > 0) {\n blocks.push(current);\n }\n\n const points: Record<string, Vec3> = {};\n const segments: [string, string][] = [];\n let autoName = 0;\n\n for (const block of blocks) {\n if (block.length % 2 !== 0) {\n throw new Error(\"KPOINTS line-mode segments must come in pairs of lines\");\n }\n for (let i = 0; i < block.length; i += 2) {\n const start = registerPathPoint(points, parsePathPoint(block[i]), ++autoName);\n const stop = registerPathPoint(points, parsePathPoint(block[i + 1]), ++autoName);\n segments.push([start, stop]);\n }\n }\n\n const density =\n Number.isFinite(pointsPerLine) && pointsPerLine > 0\n ? Math.round(pointsPerLine)\n : undefined;\n\n return { kind: \"path\", points, segments, density };\n}\n\n/* Parse a line-mode point row: x y z [label]; labels may follow \"!\". /\nfunction parsePathPoint(line: string): {\n coordinate: Vec3;\n label?: string;\n} {\n const bang = line.indexOf(\"!\");\n const content = bang === -1 ? line : line.slice(0, bang);\n const comment = bang === -1 ? \"\" : line.slice(bang + 1).trim();\n\n const tokens = content.trim().split(/\\s+/);\n if (tokens.length < 3 \|\| tokens.length > 4) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n const values = tokens.slice(0, 3).map(Number);\n if (values.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n return {\n coordinate: [values[0], values[1], values[2]],\n label: comment \|\| tokens[3],\n };\n}\n\n/* Register a path point by name, auto-naming unlabeled points. /\nfunction registerPathPoint(\n points: Record<string, Vec3>,\n point: { coordinate: Vec3; label?: string },\n autoName: number,\n): string {\n const name = point.label ?? `k${autoName}`;\n const existing = points[name];\n if (existing !== undefined && !vecApproxEqual(existing, point.coordinate)) {\n throw new Error(\n `KPOINTS label '${name}' is used for two different k-points`,\n );\n }\n points[name] = point.coordinate;\n return name;\n}\n\nfunction vecApproxEqual(a: Vec3, b: Vec3): boolean {\n return a.every((x, i) => Math.abs(x - b[i]) < 1e-9);\n}\n\n/* Parse a coordinate system name (full or abbreviated, any case). /\nfunction parseCoordinateSystem(line: string): KPointSet[\"coordinateSystem\"] {\n const cs = line.toLowerCase();\n if (cs === \"reciprocal\" \|\| cs === \"frac\" \|\| cs === \"r\") return \"reciprocal\";\n if (cs === \"cartesian\" \|\| cs === \"cart\" \|\| cs === \"c\") return \"cartesian\";\n throw new Error(`Unknown KPOINTS coordinate system '${line}'`);\n}\n\n/\n Parse a single k-point row: x y z [weight] [label]. The weight defaults to 1\n * and a trailing label (as produced by some generators) is ignored.\n /\nfunction parsePointLine(line: string): { coordinate: Vec3; weight: number } {\n const tokens = line.split(/\\s+/);\n if (tokens.length < 3) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n const values = tokens.map(Number);\n const required = tokens.length >= 4 ? values.slice(0, 4) : values.slice(0, 3);\n if (required.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS point: '${line}'`);\n }\n return {\n coordinate: [values[0], values[1], values[2]],\n weight: tokens.length >= 4 ? values[3] : 1,\n };\n}\n\n/* Parse a line of three numbers, e.g. the mesh or shift row. /\nfunction parseVec3(line: string, what: string): Vec3 {\n const values = line.split(/\\s+/).map(Number);\n if (values.length !== 3 \|\| values.some((v) => Number.isNaN(v))) {\n throw new Error(`Invalid KPOINTS ${what}: '${line}'`);\n }\n return [values[0], values[1], values[2]];\n}\n\n/\n Offset applied to each axis so a Monkhorst-Pack grid is symmetric about the\n * origin. KGrid index [i, j, k] sits at origin + [i/nx, j/ny, k/nz], while MP\n * points are at (2i - n - 1) / 2n, so the origin is (1 - n) / 2n per axis.\n /\nfunction monkhorstOrigin(mesh: GridShape, shift: Vec3): Vec3 {\n const offset = (n: number, s: number) => (1 - n) / (2 n) + s;\n return [\n offset(mesh[0], shift[0]),\n offset(mesh[1], shift[1]),\n offset(mesh[2], shift[2]),\n ];\n}\n\n/*\n Serialize k-point data back to a VASP KPOINTS file.\n \n Grids are written as automatic subdivision meshes. K-point sets are\n * canonicalized to a mesh when their points form a regular grid with uniform\n * weights (only in reciprocal coordinates); otherwise they are written as an\n * explicit list. Paths are written in reciprocal line mode, interpolating\n * `pointsPerLine` k-points per segment (default 40 when omitted; falls back\n * to `KPath.density` if set).\n /\nexport function toKPOINTS(\n data: KPoints,\n pointsPerLine?: number,\n): string {\n switch (data.kind) {\n case \"grid\":\n return serializeGrid(data);\n case \"path\":\n return serializePath(data, pointsPerLine);\n case \"points\":\n return serializePointSet(data);\n }\n}\n\n/\n Serialize a mesh, inferring the scheme from the origin: a grid whose origin\n * is the canonical Monkhorst-Pack offset (1 - n) / 2n for its mesh is written\n * as a Monkhorst-Pack file, anything else as a Gamma-centered file with the\n * origin as the shift. Either way the generated k-point mesh is identical.\n /\nfunction serializeGrid({ mesh, origin, scheme }: KGrid): string {\n const shift = scheme === \"monkhorst-pack\" ? [0, 0, 0] : origin;\n\n return [\n GRID_COMMENT,\n \"0\",\n scheme === \"monkhorst-pack\" ? \"Monkhorst-Pack\" : \"Gamma\",\n mesh.join(\" \"),\n shift.join(\" \"),\n ].join(\"\\n\");\n}\n\n/* Serialize an explicit k-point list, canonicalizing to a mesh if possible. /\nfunction serializePointSet(data: KPointSet): string {\n const grid = detectGrid(data);\n if (grid) {\n return serializeGrid(grid);\n }\n\n const coordinateSystem =\n data.coordinateSystem === \"cartesian\" ? \"Cartesian\" : \"Reciprocal\";\n const rows = data.points.map(\n (p, i) => `${p.coordinate.join(\" \")} ${data.weights?.[i] ?? 1}`,\n );\n\n return [\n LIST_COMMENT,\n String(data.points.length),\n coordinateSystem,\n ...rows,\n ].join(\"\\n\");\n}\n\n/\n Serialize a band path in reciprocal line mode. The number of points per line\n * is not part of {@link KPath} and is written with this default.\n /\nconst DEFAULT_POINTS_PER_LINE = 40;\n\nfunction serializePath(\n { points, segments, density: pathDensity }: KPath,\n pointsPerLine?: number,\n): string {\n const density =\n pointsPerLine !== undefined\n ? Math.max(1, Math.round(pointsPerLine))\n : pathDensity !== undefined\n ? Math.max(1, Math.round(pathDensity))\n : DEFAULT_POINTS_PER_LINE;\n\n const rows: string[] = [];\n for (const [start, stop] of segments) {\n rows.push(`${points[start].join(\" \")} ${start}`);\n rows.push(`${points[stop].join(\" \")} ${stop}`);\n rows.push(\"\");\n }\n rows.pop();\n\n return [\n \"Band path\",\n String(density),\n \"Line-mode\",\n \"Reciprocal\",\n ...rows,\n ].join(\"\\n\");\n}\n\n/\n Detect whether a reciprocal-coordinate point set is a regular grid.\n * Returns the grid, or null if the set is not a uniform mesh (non-uniform\n * weights, Cartesian coordinates, or irregular point spacing).\n /\nfunction detectGrid(data: KPointSet): KGrid \| null {\n if (data.coordinateSystem === \"cartesian\") return null;\n\n const weights = data.weights;\n if (weights && !weights.every((w) => Math.abs(w - weights[0]) < 1e-12)) {\n return null;\n }\n\n const axes: number[][] = [[], [], []];\n for (const { coordinate } of data.points) {\n for (let i = 0; i < 3; i++) {\n if (!axes[i].some((u) => Math.abs(u - coordinate[i]) < 1e-12)) {\n axes[i].push(coordinate[i]);\n }\n }\n }\n for (const axis of axes) {\n axis.sort((a, b) => a - b);\n }\n\n const mesh: GridShape = [axes[0].length, axes[1].length, axes[2].length];\n if (mesh[0] mesh[1] * mesh[2] !== data.points.length) return null;\n\n // Each axis must be evenly spaced with step 1/n from the first value.\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < mesh[i]; j++) {\n if (Math.abs(axes[i][j] - (axes[i][0] + j / mesh[i])) > 1e-9) {\n return null;\n }\n }\n }\n\n return {\n kind: \"grid\",\n mesh,\n origin: [axes[0][0], axes[1][0], axes[2][0]],\n scheme: \"gamma-centered\",\n };\n}\n","import type { KPath, KPoints, Vec3 } from \"../../kpoints/kpoints\";\n\n// ──────────────────────────────────────────────────────────────────────\n// CRYSTAL D3 BAND format\n// https://www.crystal.unito.it/Manuals/crystal17.pdf\n//\n// Format (for a band-structure path), per the CRYSTAL manual and\n// https://tutorials.crystalsolutions.eu (keyword BAND):\n// BAND\n// <title>\n// <nseg> <ISHR> <totk> <first_band> <last_band> <write_unit25> <print> !<comment>\n// x1 y1 z1 x2 y2 z2 !Segment_name\n// ...\n//\n// Header numbers:\n// nseg number of segments in the reciprocal-space path\n// ISHR shrinking factor; segment coordinates are multiples of 1/ISHR\n// totk total number of k points along the path\n// first_band first band to be saved\n// last_band last band to be saved\n// write_unit25 if 1, write the bands on fortran unit 25\n// print printing options\n//\n// Each segment line has 6 reciprocal-space coordinates (start, end)\n// followed by an optional `!` comment indicating the segment label.\n// The first header number is the number of segment lines.\n// ──────────────────────────────────────────────────────────────────────\n\nconst BAND_HEADER = /^BAND\\s$/i;\n\n/* Default number of k-points interpolated per band-path segment. /\nconst DEFAULT_POINTS_PER_SEGMENT = 40;\n\nfunction stripComment(line: string): string {\n let cut = line.length;\n const bang = line.indexOf(\"!\");\n const hash = line.indexOf(\"#\");\n if (bang !== -1) cut = Math.min(cut, bang);\n if (hash !== -1) cut = Math.min(cut, hash);\n return line.slice(0, cut).trim();\n}\n\nfunction extractComment(line: string): string {\n const bang = line.indexOf(\"!\");\n const content = bang === -1 ? line : line.slice(0, bang);\n const explicit = bang === -1 ? \"\" : line.slice(bang + 1).trim();\n if (explicit !== \"\") return explicit;\n\n // No `!` marker: any tokens after the first six (the segment coordinates)\n // are treated as the segment label, e.g. \"GAMMA -> C\".\n const tokens = content.trim().split(/\\s+/).filter((t) => t !== \"\");\n for (let i = 6; i < tokens.length; i++) {\n if (!NUMERIC_TOKEN.test(tokens[i])) {\n return tokens.slice(i).join(\" \");\n }\n }\n return \"\";\n}\n\nconst NUMERIC_TOKEN = /^[-+]?\\d\\.?\\d+(?:[eE][-+]?\\d+)?$/;\n\nfunction parseVec6(line: string): [Vec3, Vec3] {\n const stripped = stripComment(line);\n const tokens = stripped.split(/\\s+/).filter(Boolean);\n if (tokens.length < 6) {\n throw new Error(`Invalid D3 BAND segment line: '${line}'`);\n }\n const nums = tokens.slice(0, 6).map(Number);\n if (nums.some(Number.isNaN)) {\n throw new Error(`Invalid D3 BAND segment line: '${line}'`);\n }\n return [\n [nums[0], nums[1], nums[2]],\n [nums[3], nums[4], nums[5]],\n ];\n}\n\nfunction formatVec6(start: Vec3, end: Vec3, comment: string): string {\n const cmt = comment ? ` ${comment}` : \"\";\n return `${start.join(\" \")} ${end.join(\" \")}${cmt}`;\n}\n\n/*\n Parse a CRYSTAL D3 BAND input file into the canonical k-point representation.\n \n Segments are returned as a {@link KPath}. Coordinates are in reciprocal\n * lattice units (2π/a); converting to fractional coordinates requires the\n * lattice. The returned path stores the raw coordinates.\n \n @param text The D3 BAND file content.\n /\nexport function fromCrystalD3(text: string): KPath {\n // Only trim leading/trailing blank lines: an empty title line is valid\n // and must stay in its slot (line 2).\n const raw = text.split(\"\\n\");\n let first = 0;\n let last = raw.length - 1;\n while (first < raw.length && raw[first].trim() === \"\") first++;\n while (last > first && raw[last].trim() === \"\") last--;\n const lines = raw.slice(first, last + 1);\n\n if (lines.length < 3) {\n throw new Error(\"D3 BAND file is too short\");\n }\n\n if (!BAND_HEADER.test(lines[0].trim())) {\n throw new Error(\"D3 BAND file must start with 'BAND'\");\n }\n\n // Line 2: title (ignored for canonical representation)\n const _title = lines[1].trim();\n\n // Line 3: header — first number is the number of segments\n const headerNums = stripComment(lines[2])\n .split(/\\s+/)\n .filter(Boolean)\n .map(Number);\n if (headerNums.length < 1 \|\| headerNums.some(Number.isNaN)) {\n throw new Error(\"Invalid D3 BAND header line\");\n }\n const nks = headerNums[0];\n\n if (lines.length < 3 + nks) {\n throw new Error(\n `D3 BAND header declares ${nks} segments but only ${lines.length - 3} lines remain`,\n );\n }\n\n const points: Record<string, Vec3> = {};\n const nameByCoord = new Map<string, string>();\n const segments: [string, string][] = [];\n let autoName = 0;\n\n const nameFor = (coord: Vec3, preferred?: string): string => {\n const key = coord.join(\" \");\n const existing = nameByCoord.get(key);\n if (existing !== undefined) return existing;\n if (preferred !== undefined) {\n const prev = points[preferred];\n if (prev !== undefined && !vecApproxEqual(prev, coord)) {\n throw new Error(\n `D3 BAND: label '${preferred}' used for two different coordinates`,\n );\n }\n nameByCoord.set(key, preferred);\n points[preferred] = coord;\n return preferred;\n }\n const name = `k${++autoName}`;\n nameByCoord.set(key, name);\n points[name] = coord;\n return name;\n };\n\n for (let i = 3; i < 3 + nks; i++) {\n const line = lines[i];\n const [start, end] = parseVec6(line);\n const comment = extractComment(line);\n\n // Parse comment like \"GAMMA -> C\" or \"C_2 -> Y_2\"\n let startName: string \| undefined;\n let endName: string \| undefined;\n if (comment.includes(\"->\")) {\n const parts = comment.split(\"->\").map((s) => s.trim());\n startName = parts[0] \|\| undefined;\n endName = parts[1] \|\| undefined;\n }\n\n segments.push([\n nameFor(start, startName),\n nameFor(end, endName),\n ]);\n }\n\n return { kind: \"path\", points, segments };\n}\n\nfunction vecApproxEqual(a: Vec3, b: Vec3): boolean {\n return a.every((x, i) => Math.abs(x - b[i]) < 1e-6);\n}\n\n/\n Serialize canonical k-point data as a CRYSTAL D3 BAND input file.\n \n The path segments are written as start/end coordinate pairs with inline\n * segment name comments. The header line follows the CRYSTAL BAND format:\n * segment count, shrinking factor 1 (fractional reciprocal coordinates),\n * the total number of k points (segments × points per segment), a\n * 1st-to-0th band range, unit-25 writing on, and no printing options.\n \n @param data The canonical k-point data. Must be a {@link KPath}.\n * @param title Optional title line (defaults to empty).\n * @param pointsPerSegment Number of k points interpolated per segment.\n * Defaults to the path's own `density` when set,\n * otherwise 40.\n /\nexport function toCrystalD3(\n data: KPoints,\n title = \"\",\n pointsPerSegment?: number,\n): string {\n if (data.kind !== \"path\") {\n throw new Error(\"toCrystalD3 only supports KPath data\");\n }\n\n const segmentLines: string[] = [];\n for (const [startName, endName] of data.segments) {\n const start = data.points[startName];\n const end = data.points[endName];\n if (!start \|\| !end) {\n throw new Error(\n `KPath references unknown point '${startName}' or '${endName}'`,\n );\n }\n segmentLines.push(formatVec6(start, end, `${startName} -> ${endName}`));\n }\n\n const nseg = data.segments.length;\n const density =\n pointsPerSegment !== undefined\n ? Math.max(1, Math.round(pointsPerSegment))\n : data.density !== undefined\n ? Math.max(1, Math.round(data.density))\n : DEFAULT_POINTS_PER_SEGMENT;\n\n // TODO(check): CRYSTAL's exact joint-dedup rule for the total k-point count\n // is unverified. nseg × points-per-segment matches the MgO tutorial\n // (4 segments → 60 total = 4 × 15) and mirrors the VASP/QE density semantics.\n const totalPoints = nseg density;\n // [nseg, ISHR=1, totk, first_band, last_band, write_unit25, print]\n const header = `${nseg} 1 ${totalPoints} 1 0 1 0`;\n\n return [\"BAND\", title, header, ...segmentLines].join(\"\\n\");\n}\n","/*\n First-class pseudopotential data model.\n \n This module defines the canonical in-memory representation of a\n * pseudopotential. The model is derived from the UPF v2.0.1 format (the\n * superset of all supported formats) and every other format is handled by an\n * adapter in `lib/core/io/pseudo/` that converts into / out of this type.\n \n Canonical in-memory units: Rydberg (energy), Bohr (length) — i.e. the\n * UPF-native units. Adapters for Hartree-based formats (PSP8, FHI/CPI, PSML,\n * GTH) convert energies on parse (×2) and back on serialize (×0.5). Both\n * factors are exact powers of two, so round-trips stay bit-exact.\n /\n\n/* Pseudopotential type identifiers in UPF format. /\nexport type PseudopotentialType = \"NC\" \| \"SL\" \| \"1/r\" \| \"US\" \| \"PAW\";\n\n/* Relativistic treatment identifiers. \"no\" is observed in the wild (FHI98PP). /\nexport type RelativisticType = \"scalar\" \| \"full\" \| \"nonrelativistic\" \| \"no\";\n\n/* UPF version string. Only set when the source format is UPF. /\nexport type UPFVersion = \"1.0.0\" \| \"2.0.1\";\n\n/* Source format identifier for interconversion. /\nexport type PseudopotentialFormat =\n \| \"UPF1\"\n \| \"UPF2\"\n \| \"PSP8\"\n \| \"PSML\"\n \| \"CPI\"\n \| \"GTH\"\n \| \"HGH\";\n\n/* Canonical in-memory energy unit (Rydberg). /\nexport type EnergyUnit = \"Ry\";\n\n/* Canonical in-memory length unit (Bohr). /\nexport type LengthUnit = \"Bohr\";\n\n/* Units attached to every first-class pseudopotential object. /\nexport interface PseudopotentialUnits {\n energy: EnergyUnit;\n length: LengthUnit;\n}\n\n/* The canonical unit system (Ry / Bohr). /\nexport const CANONICAL_UNITS: PseudopotentialUnits = {\n energy: \"Ry\",\n length: \"Bohr\",\n};\n\n/* Header attributes from PP_HEADER section. /\nexport interface PseudopotentialHeader {\n /* Generation code identifier. /\n generated?: string;\n /* Author of the pseudopotential. /\n author?: string;\n /* Generation date. /\n date?: string;\n /* Brief description. /\n comment?: string;\n /* Chemical element symbol (\"\" when the source format carries none, e.g. raw .cpi). /\n element: string;\n /* Pseudopotential type. /\n pseudoType: PseudopotentialType;\n /* Level of relativistic formalism. /\n relativistic: RelativisticType;\n /* True if ultrasoft (Vanderbilt) pseudopotential. /\n isUltrasoft: boolean;\n /* True if PAW dataset. /\n isPaw: boolean;\n /* True if Coulomb 1/r potential. /\n isCoulomb: boolean;\n /* True if spin-orbit information present. /\n hasSo: boolean;\n /* True if all-electron orbitals present. /\n hasWfc: boolean;\n /* True if GIPAW data present. /\n hasGipaw: boolean;\n /* True if PAW used as GIPAW. /\n pawAsGipaw: boolean;\n /* True if non-linear core correction present. /\n coreCorrection: boolean;\n /* DFT functional identifier. /\n functional: string;\n /* Valence charge. /\n zValence: number;\n /* Total pseudo-valence energy (Ry). /\n totalPsenergy: number;\n /* Suggested wavefunction cutoff (Ry). /\n wfcCutoff: number;\n /* Suggested charge density cutoff (Ry). /\n rhoCutoff: number;\n /* Maximum angular momentum of valence orbitals. /\n lMax: number;\n /* Maximum angular momentum of atomic charge density. /\n lMaxRho: number;\n /* Angular momentum of local channel. /\n lLocal: number;\n /* Number of radial mesh points. /\n meshSize: number;\n /* Number of atomic wavefunctions. /\n numberOfWfc: number;\n /* Number of Kleinman-Bylander projectors. /\n numberOfProj: number;\n /* Numeric XC functional code (PSP8 pspxc). /\n xcCode?: number;\n /* Spin-orbit extension switch (PSP8). /\n extensionSwitch?: number;\n /* Pseudopotential well radius r2well (PSP8/FHI ABINIT header). /\n r2well?: number;\n /* Core charge radius rchrg (PSP8 ABINIT header). /\n rchrg?: number;\n /* Core charge model flag fchrg (PSP8 ABINIT header). /\n fchrg?: number;\n /* Core charge qchrg (PSP8 ABINIT header). /\n qchrg?: number;\n}\n\n/* Radial mesh parameters and data from PP_MESH section. /\nexport interface PseudopotentialMesh {\n /* Grid type discriminator. /\n gridType?: \"logarithmic\" \| \"linear\" \| \"custom\";\n /* Logarithmic grid spacing parameter dx. /\n dx?: number;\n /* Number of mesh points. /\n mesh?: number;\n /* Minimum x value for logarithmic grid. /\n xmin?: number;\n /* Maximum radial coordinate. /\n rmax: number;\n /* Nuclear charge for grid generation. /\n zmesh?: number;\n /* Radial grid points r(i) in Bohr. /\n r: Float64Array;\n /* Radial integration weights rab(i). /\n rab: Float64Array;\n}\n\n/* Local potential from PP_LOCAL section. /\nexport interface PseudopotentialLocal {\n /* Local potential vloc(mesh) in Ry. /\n vloc: Float64Array;\n}\n\n/* A single Kleinman-Bylander projector from PP_BETA section. /\nexport interface BetaProjector {\n /* 1-based position of this projector in the file ordering. /\n index?: number;\n /* Angular momentum of this projector. /\n angularMomentum: number;\n /* Number of mesh points for this projector. /\n cutoffRadiusIndex?: number;\n /* Cutoff radius in Bohr. /\n cutoffRadius?: number;\n /* Norm-conserving radius (US only). /\n normConservingRadius?: number;\n /* Ultrasoft cutoff radius. /\n ultrasoftCutoffRadius: number;\n /* Projector label. /\n label: string;\n /* Projector values beta(r) * r. /\n beta: Float64Array;\n}\n\n/* A single Q_ij^L augmentation function from PP_QIJL.i.j.L (USPP/PAW). /\nexport interface QijlFunction {\n /* First projector index (1-based). /\n i: number;\n /* Second projector index (1-based). /\n j: number;\n /* Augmentation angular momentum. /\n l: number;\n /* Augmentation function values on the radial mesh. /\n qijl: Float64Array;\n}\n\n/* Nonlocal pseudopotential data from PP_NONLOCAL section. /\nexport interface PseudopotentialNonlocal {\n /* Array of beta projectors. /\n betas: BetaProjector[];\n /* D_ij matrix entries. Format: [nb, mb, value in Ry] triples (1-based). /\n dij: Array<[number, number, number]>;\n /* Number of Q function expansion coefficients. /\n nqf?: number;\n /* Augmentation data (USPP/PAW). /\n augmentation?: AugmentationData;\n}\n\n/* Augmentation data from PP_AUGMENTATION section (USPP/PAW). /\nexport interface AugmentationData {\n /* Number of Q function expansion coefficients. /\n nqf?: number;\n /* Number of Q_ij composite functions (nqlc). /\n nqlc?: number;\n /* Augmentation charge shape (BESSEL, GAUSS, PSQ, etc.). /\n shape?: string;\n /* Augmentation matching radius. /\n rMatchAugfun?: number;\n /* Cutoff radius for augmentation (alias: iraug). /\n cutoffR?: number;\n /* Index of radial grid point at the augmentation cutoff radius. /\n cutoffRIndex?: number;\n /* Index of radial grid point at augmentation radius (legacy alias). /\n irc?: number;\n /* Maximum angular momentum of augmentation (accepts l_max_aug / lmax_aug). /\n lmaxAug?: number;\n /* Augmentation pseudization threshold. /\n augmentationEpsilon?: number;\n /* Q_ij norms from PP_Q section. /\n q?: Float64Array;\n /* Electrostatic multipoles from PP_MULTIPOLES section. /\n multipoles?: Float64Array;\n /* Taylor expansion coefficients from PP_QFCOEFF section. /\n qfcoeff?: Float64Array;\n /* Inner radii for Q function from PP_RINNER section. /\n rinner?: Float64Array;\n /* Whether augmentation charge depends on angular momentum. /\n qWithL?: boolean;\n /* Augmentation charge functions from PP_QIJL.i.j.L sections. /\n qijl?: QijlFunction[];\n}\n\n/* Atomic wavefunction from PP_CHI section. /\nexport interface PseudopotentialWfc {\n /* Angular momentum quantum number. /\n l: number;\n /* Occupation number. /\n occupation: number;\n /* Wavefunction label (e.g. \"2S\", \"3P\"). /\n label?: string;\n /* Principal quantum number. /\n n?: number;\n /* Pseudo energy (Ry). /\n pseudoEnergy?: number;\n /* Inner cutoff radius. /\n cutoffRadius?: number;\n /* Ultrasoft cutoff radius. /\n ultrasoftCutoffRadius?: number;\n /* Wavefunction values chi(r) * r. /\n chi: Float64Array;\n}\n\n/* All-electron wavefunction from PP_FULL_WFC section (PAW). /\nexport interface FullWfc {\n /* Angular momentum quantum number. /\n l: number;\n /* Wavefunction label. /\n label: string;\n /* Wavefunction values aewfc(r) * r. /\n aewfc: Float64Array;\n}\n\n/* PAW dataset from PP_PAW section. /\nexport interface PawData {\n /* PAW data format version. /\n pawDataFormat: number;\n /* Core energy constant (Ry). /\n coreEnergy: number;\n /* Occupations of atomic orbitals. /\n occupations: Float64Array;\n /* All-electron core charge. /\n aeNlcc: Float64Array;\n /* All-electron local potential (Ry). /\n aeVloc: Float64Array;\n /* All-electron wavefunctions. /\n aeWfcs: FullWfc[];\n /* Pseudo wavefunctions for each projector. /\n psWfcs: FullWfc[];\n}\n\n/* GIPAW data from PP_GIPAW / PP_GIPAW_RECONSTRUCTION section. /\nexport interface GipawData {\n /* Which tag the data was read from (preserved for round-trip fidelity). /\n tag?: \"PP_GIPAW\" \| \"PP_GIPAW_RECONSTRUCTION\";\n /* GIPAW data format version. /\n gipawDataFormat: number;\n /* Core orbitals. /\n coreOrbitals: Array<{\n n: number;\n l: number;\n orbital: Float64Array;\n }>;\n /* AE and PS orbitals for each valence state. /\n orbitals: Array<{\n l: number;\n label: string;\n aeOrbital: Float64Array;\n psOrbital: Float64Array;\n }>;\n /* AE local potential. /\n vlocAe: Float64Array;\n /* PS local potential. /\n vlocPs: Float64Array;\n}\n\n/* A single relativistic wavefunction entry with its radial data. /\nexport interface RelativisticWfc {\n /* Total angular momentum j of the spinor. /\n jchi: number;\n index?: number;\n els?: string;\n nn?: number;\n lchi?: number;\n oc?: number;\n /* Relativistic wavefunction values (may be absent in legacy files). /\n chi?: Float64Array;\n}\n\n/* A single relativistic projector entry with its radial data. /\nexport interface RelativisticBeta {\n /* Total angular momentum j of the projector. /\n jjj: number;\n index?: number;\n lll?: number;\n /* Relativistic projector values (may be absent in legacy files). /\n beta?: Float64Array;\n}\n\n/* Spin-orbit data from PP_SPIN_ORB section. /\nexport interface SpinOrbitData {\n /* Relativistic wavefunction data. /\n relWfcs: RelativisticWfc[];\n /* Relativistic projector data. /\n relBetas: RelativisticBeta[];\n}\n\n/* GTH/HGH analytical pseudopotential parameters (energies in Ry). /\nexport interface GthData {\n /* Valence electron configuration [s, p, d, ...]. /\n nElec: number[];\n /* Local potential Gaussian radius. /\n rLoc: number;\n /* Local potential Gaussian coefficients (Ry). /\n cexpPpl: number[];\n /* Non-local projector radii per angular momentum channel. /\n rPs: number[];\n /* h-matrix elements [channel][i][j] (Ry). /\n hprj: number[][][];\n /* k-matrix elements for spin-orbit [channel][i][j] (Ry). /\n kprj?: number[][][];\n}\n\n/* Provenance metadata: where this object came from. /\nexport interface Provenance {\n /* Format the data was originally read from. /\n sourceFormat: PseudopotentialFormat;\n /* Generator program name. /\n creator?: string;\n /* Generation date. /\n date?: string;\n /* Embedded input files. /\n inputFiles?: Array<{ name: string; content: string }>;\n /* True when analytical parameters (GTH/HGH) are preserved alongside the grid. /\n analytical?: boolean;\n /* Free-form notes (e.g. appended by resampling operations). /\n notes?: string;\n}\n\n/* Complete pseudopotential data: the first-class pseudopotential object. /\nexport interface Pseudopotential {\n /* Source format this object was parsed from. /\n format: PseudopotentialFormat;\n /* UPF format version (only set for UPF1/UPF2 sources). /\n version?: UPFVersion;\n /* Canonical in-memory units (always Ry / Bohr). /\n units: PseudopotentialUnits;\n /* Provenance metadata (source format, generator, ...). /\n provenance: Provenance;\n /* Human-readable info section. /\n info?: string;\n /* Raw PP_INPUTFILE content, when present in the source. /\n inputFile?: string;\n /* Header with metadata. /\n header: PseudopotentialHeader;\n /* Radial mesh. /\n mesh: PseudopotentialMesh;\n /* Non-linear core correction charge. /\n nlcc?: Float64Array;\n /* Local potential. /\n local: PseudopotentialLocal;\n /* Semilocal potentials (NC only). /\n semilocal?: Array<{\n l: number;\n j?: number;\n vnl: Float64Array;\n }>;\n /* Nonlocal projectors and D_ij. /\n nonlocal: PseudopotentialNonlocal;\n /* Atomic pseudo-wavefunctions. /\n pswfc: PseudopotentialWfc[];\n /* Atomic all-electron wavefunctions (PAW). /\n fullWfc?: FullWfc[];\n /* Atomic charge density. /\n rhoatom: Float64Array;\n /* PAW dataset. /\n paw?: PawData;\n /* GIPAW reconstruction data. /\n gipaw?: GipawData;\n /* Spin-orbit coupling data. /\n spinOrbit?: SpinOrbitData;\n /* GTH/HGH analytical parameters (when format is GTH or HGH). /\n gth?: GthData;\n}\n","/* Parse a Fortran-style number (D-notation) to a JS number. /\nexport function parseFortranNumber(s: string): number {\n return Number.parseFloat(s.replace(/[dD]/g, \"e\"));\n}\n\n/* Parse a Fortran-style boolean string. /\nexport function parseFortranBool(s: string): boolean {\n const v = s.trim().toLowerCase();\n return v === \".true.\" \|\| v === \"true\" \|\| v === \"t\";\n}\n\n/* Parse whitespace-separated text into a Float64Array. /\nexport function parseFloat64Array(text: string): Float64Array {\n const tokens = text.trim().split(/\\s+/).filter(Boolean);\n const arr = new Float64Array(tokens.length);\n for (let i = 0; i < tokens.length; i++) {\n arr[i] = parseFortranNumber(tokens[i]);\n }\n return arr;\n}\n\n/* Parse a string to integer, trimming whitespace. /\nexport function parseIntSafe(s: string): number {\n return Number.parseInt(s.trim(), 10);\n}\n\n/* Format a number in Fortran D-notation. Preserves negative zero. /\nexport function formatFortranNumber(n: number, width = 20): string {\n // 17 significant digits: the minimum that round-trips any double\n // bit-exactly (some generators, e.g. atompaw, write 17 digits).\n const s = n.toExponential(16);\n // toExponential drops the sign of -0; restore it for round-trip fidelity.\n const signed = Object.is(n, -0) && !s.startsWith(\"-\") ? `-${s}` : s;\n const d = signed.replace(/e/, \"D\").replace(/e\\+/, \"D+\").replace(/e-/, \"D-\");\n return d.padStart(width);\n}\n\n/* Format a boolean as Fortran `.true.` / `.false.`. /\nexport function formatFortranBool(b: boolean): string {\n return b ? \".true.\" : \".false.\";\n}\n\n/* Escape special characters for XML attribute values. /\nexport function escapeXmlAttr(s: string): string {\n return s.replace(/&/g, \"&\").replace(/</g, \"<\").replace(/>/g, \">\").replace(/\"/g, \""\");\n}\n\n/* Format a Float64Array as columns of Fortran D-notation numbers. /\nexport function formatDataArray(arr: Float64Array, columns = 4): string {\n const lines: string[] = [];\n for (let i = 0; i < arr.length; i += columns) {\n const row: string[] = [];\n for (let j = 0; j < columns && i + j < arr.length; j++) {\n row.push(formatFortranNumber(arr[i + j]));\n }\n lines.push(row.join(\" \"));\n }\n return lines.join(\"\\n\");\n}\n","function e(e){return e.replace(/&(#x[0-9a-fA-F]+\|#\\d+\|amp\|lt\|gt\|quot\|apos);/g,function(e,t){if(\"amp\"===t)return\"&\";if(\"lt\"===t)return\"<\";if(\"gt\"===t)return\">\";if(\"quot\"===t)return'\"';if(\"apos\"===t)return\"'\";if(\"#\"===t[0]){var r=\"x\"===t[1]\|\|\"X\"===t[1],a=parseInt(t.slice(r?2:1),r?16:10);if(!Number.isNaN(a)&&a>=0&&a<=1114111)try{return String.fromCodePoint(a)}catch(t){return e}}return e})}function t(e){return e.replace(/&/g,\"&\").replace(/</g,\"<\").replace(/>/g,\">\")}function r(e){return e.replace(/&/g,\"&\").replace(/</g,\"<\").replace(/>/g,\">\").replace(/\"/g,\""\").replace(/'/g,\"'\")}function a(t,r){var 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if(r.parseNode)for(E=W();f&&\"object\"==typeof E&&E&&N(E.tagName);)E=W();else E=x(\"\");if(r.filter&&Array.isArray(E)&&(E=o(E,r.filter)),r.simplify){return n(Array.isArray(E)?E:[E])}return r.setPos&&\"object\"==typeof E&&!Array.isArray(E)&&(E.pos=a),E}function n(e){if(\"string\"==typeof e)return n(a(e));if(!Array.isArray(e))throw new TypeError(\"simplify() expects parsed node array or XML string\");var t={};if(!e.length)return\"\";if(1===e.length&&\"string\"==typeof e[0])return e[0];for(var r in e.forEach(function(e){if(\"object\"==typeof e){t[e.tagName]\|\|(t[e.tagName]=[]);var r=n(e.children);t[e.tagName].push(r),Object.keys(e.attributes).length&&\"object\"==typeof r&&!Array.isArray(r)&&(r._attributes=e.attributes)}}),t)1==t[r].length&&(t[r]=t[r][0]);return t}function i(e,t={}){var r={};return e.length?1===e.length&&\"string\"==typeof e[0]?Object.keys(t).length?{_attributes:t,value:e[0]}:e[0]:(e.forEach(function(e){if(\"object\"==typeof e){r[e.tagName]\|\|(r[e.tagName]=[]);var t=i(e.children\|\|[],e.attributes);r[e.tagName].push(t),Object.keys(e.attributes).length&&\"object\"==typeof t&&!Array.isArray(t)&&(t._attributes=e.attributes)}}),r):r}function o(e,t,r=0,a=\"\"){var n=[];return function e(r,a,i){r.forEach(function(r,o){\"object\"==typeof r&&(t(r,o,a,i)&&n.push(r),r.children&&e(r.children,a+1,(i?i+\".\":\"\")+o+\".\"+r.tagName))})}(e,r,a),n}function c(e,a){if(!e)return\"\";var n=!!(a=a\|\|{}).encodeEntities,i=void 0!==a.keepWhitespace?!!a.keepWhitespace:!!a.keepWhitespaces,o=!1!==a.selfCloseEmpty,c=\"\";function s(e){if(e)for(var r=0;r<e.length;r++){var a=e[r];if(\"string\"==typeof a){var o=i?a:a.trim();c+=n?t(o):o}else a&&f(a)}}function f(e){if(e){for(var t in c+=\"<\"+e.tagName,e.attributes){var a=e.attributes[t];null===a?c+=\" \"+t:n?c+=\" \"+t+'=\"'+r(a.trim())+'\"':-1===a.indexOf('\"')?c+=\" \"+t+'=\"'+a.trim()+'\"':c+=\" \"+t+\"='\"+a.trim()+\"'\"}if(\"?\"!==e.tagName[0])!0!==e.selfClosed&&(!o\|\|function(e){if(!e\|\|0===e.length)return!1;for(var t=0;t<e.length;t++){var r=e[t];if(\"string\"==typeof r){if((i?r:r.trim()).length>0)return!0}else if(r)return!0}return!1}(e.children))?(c+=\">\",s(e.children),c+=\"</\"+e.tagName+\">\"):c+=\"/>\";else{if(e.children&&e.children.length){var f=e.children.filter(function(e){return\"string\"==typeof e}).join(\" \").trim();f.length>0&&(c+=\" \"+f)}c+=\"?>\"}}}return s(Array.isArray(e)?e:[e]),c}function s(e){if(Array.isArray(e)){var t=\"\";return e.forEach(function(e){t=(t+=\" \"+s(e)).trim()}),t}return\"object\"==typeof e&&null!==e?s(e.children):\" \"+e}function f(e,t,r){var i=a(e,{attrValue:t});return r?n(i):i[0]}function u(e,t,r){const i=a(e,{attrName:\"class\",attrValue:\"[a-zA-Z0-9- ]\"+t+\"[a-zA-Z0-9- ]\"});return r?n(i):i}function l(e){return\"string\"==typeof e}function h(e){return\"object\"==typeof e&&null!==e&&\"tagName\"in e}export{o as filter,f as getElementById,u as getElementsByClassName,h as isElementNode,l as isTextNode,a as parse,n as simplify,i as simplifyLostLess,c as stringify,s as toContentString};\n","import { parse as parseTxml } from \"txml/txml\";\n\nimport {\n parseFortranNumber,\n parseIntSafe,\n parseFortranBool,\n} from \"./fortran-helpers\";\n\n/** An XML node: attributes under `@_<name>`, leaf text under `#text`. /\nexport type XmlNode = Record<string, any>;\n\n/* Get an attribute value from an XML node. /\nexport function attr(node: XmlNode \| undefined, name: string): string {\n return node?.[`@_${name}`] ?? \"\";\n}\n\n/* Get an attribute as a Fortran-number. /\nexport function attrNum(\n node: XmlNode \| undefined,\n name: string,\n fallback = 0,\n): number {\n const v = attr(node, name);\n return v ? parseFortranNumber(v) : fallback;\n}\n\n/* Get an attribute as an integer. /\nexport function attrInt(\n node: XmlNode \| undefined,\n name: string,\n fallback = 0,\n): number {\n const v = attr(node, name);\n return v ? parseIntSafe(v) : fallback;\n}\n\n/* Get an attribute as a Fortran boolean. /\nexport function attrBool(node: XmlNode \| undefined, name: string): boolean {\n return parseFortranBool(attr(node, name) \|\| \".false.\");\n}\n\n/* Extract text content from an XML node. /\nexport function textOf(node: XmlNode \| string \| undefined): string {\n if (typeof node === \"string\") return node;\n if (node && \"#text\" in node) return String(node[\"#text\"]);\n return \"\";\n}\n\n/* Normalize a value or array to an array (ensuring T[]). /\nexport function toArray<T>(v: T \| T[] \| undefined \| null): T[] {\n if (Array.isArray(v)) return v;\n if (v == null) return [];\n return [v];\n}\n\n/* Object entries of an XML node, typed for section iteration. /\nexport function entries(node: XmlNode \| undefined): Array<[string, XmlNode]> {\n return Object.entries(node ?? {}) as Array<[string, XmlNode]>;\n}\n\nconst ENTITY_RE = /&(amp\|lt\|gt\|quot\|apos\|#\\d+\|#x[\\da-fA-F]+);/g;\n\n/\n Decode XML entities. txml leaves them raw, so the adapter decodes the\n * predefined set plus decimal/hex character references.\n /\nexport function decodeEntities(s: string): string {\n if (!s.includes(\"&\")) return s;\n return s.replace(ENTITY_RE, (m, body: string) => {\n switch (body) {\n case \"amp\":\n return \"&\";\n case \"lt\":\n return \"<\";\n case \"gt\":\n return \">\";\n case \"quot\":\n return '\"';\n case \"apos\":\n return \"'\";\n default: {\n const hex = body[1] === \"x\" \|\| body[1] === \"X\";\n const code = parseInt(body.slice(hex ? 2 : 1), hex ? 16 : 10);\n return Number.isFinite(code) ? String.fromCodePoint(code) : m;\n }\n }\n });\n}\n\ninterface TxmlNode {\n tagName: string;\n attributes: Record<string, string>;\n children: Array<TxmlNode \| string>;\n}\n\nfunction convertNode(node: TxmlNode, out: XmlNode): void {\n for (const k of Object.keys(node.attributes)) {\n // trimValues equivalent: attribute values are trimmed.\n out[`@_${k}`] = decodeEntities(node.attributes[k]).trim();\n }\n for (const child of node.children) {\n if (typeof child === \"string\") {\n if (child.trim() === \"\") continue;\n const text = decodeEntities(child);\n const prev = out[\"#text\"];\n out[\"#text\"] = prev === undefined ? text : `${prev as string}${text}`;\n continue;\n }\n // Skip processing instructions (e.g. <?xml ...?>).\n if (child.tagName.startsWith(\"?\")) continue;\n appendChild(out, child.tagName, convertElement(child));\n }\n if (typeof out[\"#text\"] === \"string\") out[\"#text\"] = out[\"#text\"].trim();\n}\n\n/\n Convert one element, mirroring fast-xml-parser value collapsing:\n * attribute-less leaves become bare strings (\"\" when empty).\n /\nfunction convertElement(node: TxmlNode): XmlNode \| string {\n const hasAttrs = Object.keys(node.attributes).length > 0;\n if (!hasAttrs) {\n const parts: string[] = [];\n for (const child of node.children) {\n if (typeof child === \"string\") {\n if (child.trim() !== \"\") parts.push(decodeEntities(child));\n } else if (!child.tagName.startsWith(\"?\")) {\n // Has element children: fall through to object form below.\n const out: XmlNode = {};\n convertNode(node, out);\n return out;\n }\n }\n return parts.join(\"\").trim();\n }\n const out: XmlNode = {};\n convertNode(node, out);\n return out;\n}\n\nfunction appendChild(out: XmlNode, tag: string, sub: XmlNode \| string): void {\n const existing = out[tag];\n if (existing === undefined) out[tag] = sub;\n else if (Array.isArray(existing)) existing.push(sub);\n else out[tag] = [existing, sub];\n}\n\n/\n Parse XML text into an XmlNode tree (txml-backed).\n \n Equivalent semantics to the previous fast-xml-parser configuration:\n * attributes under `@_`, leaf text under `#text`, repeated tags as arrays.\n * Singletons stay objects — use toArray() when iterating sections.\n /\nexport function parseXml(text: string): XmlNode {\n const doc: XmlNode = {};\n for (const node of parseTxml(text) as TxmlNode[]) {\n if (typeof node === \"string\") continue;\n if (node.tagName.startsWith(\"?\")) continue;\n appendChild(doc, node.tagName, convertElement(node));\n }\n return doc;\n}\n","import type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n FullWfc,\n AugmentationData,\n PawData,\n GipawData,\n SpinOrbitData,\n RelativisticWfc,\n RelativisticBeta,\n QijlFunction,\n PseudopotentialType,\n RelativisticType,\n UPFVersion,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFortranBool,\n parseFloat64Array,\n parseIntSafe,\n formatFortranNumber,\n formatFortranBool,\n escapeXmlAttr,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n attrBool,\n textOf,\n toArray,\n entries,\n parseXml,\n} from \"./xml-helpers\";\n\nfunction parseData(text: string): Float64Array {\n return parseFloat64Array(text);\n}\n\n/* Parse optional radial data: undefined when the element has no text. /\nfunction parseOptionalData(text: string): Float64Array \| undefined {\n return text.trim() ? parseData(text) : undefined;\n}\n\n// ── Section parsers ────────────────────────────────────────────────\n\nfunction parseHeader(node: XmlNode): PseudopotentialHeader {\n return {\n generated: attr(node, \"generated\") \|\| undefined,\n author: attr(node, \"author\") \|\| undefined,\n date: attr(node, \"date\") \|\| undefined,\n comment: attr(node, \"comment\") \|\| undefined,\n element: attr(node, \"element\").trim(),\n pseudoType: (attr(node, \"pseudo_type\") as PseudopotentialType) \|\| \"NC\",\n relativistic: (attr(node, \"relativistic\") as RelativisticType) \|\| \"scalar\",\n isUltrasoft: attrBool(node, \"is_ultrasoft\"),\n isPaw: attrBool(node, \"is_paw\"),\n isCoulomb: attrBool(node, \"is_coulomb\"),\n hasSo: attrBool(node, \"has_so\"),\n hasWfc: attrBool(node, \"has_wfc\"),\n hasGipaw: attrBool(node, \"has_gipaw\"),\n pawAsGipaw: attrBool(node, \"paw_as_gipaw\"),\n coreCorrection: attrBool(node, \"core_correction\"),\n functional: attr(node, \"functional\"),\n zValence: attrNum(node, \"z_valence\"),\n totalPsenergy: attrNum(node, \"total_psenergy\"),\n wfcCutoff: attrNum(node, \"wfc_cutoff\"),\n rhoCutoff: attrNum(node, \"rho_cutoff\"),\n lMax: attrInt(node, \"l_max\"),\n lMaxRho: attrInt(node, \"l_max_rho\"),\n lLocal: attrInt(node, \"l_local\", -1),\n meshSize: attrInt(node, \"mesh_size\"),\n numberOfWfc: attrInt(node, \"number_of_wfc\"),\n numberOfProj: attrInt(node, \"number_of_proj\"),\n };\n}\n\nfunction parseMesh(node: XmlNode): PseudopotentialMesh {\n const dx = attr(node, \"dx\") ? attrNum(node, \"dx\") : undefined;\n return {\n gridType: dx != null ? \"logarithmic\" : \"custom\",\n dx,\n mesh: attr(node, \"mesh\") ? attrInt(node, \"mesh\") : undefined,\n xmin: attr(node, \"xmin\") ? attrNum(node, \"xmin\") : undefined,\n rmax: attrNum(node, \"rmax\"),\n zmesh: attr(node, \"zmesh\") ? attrNum(node, \"zmesh\") : undefined,\n r: parseData(textOf(node[\"PP_R\"])),\n rab: parseData(textOf(node[\"PP_RAB\"])),\n };\n}\n\nfunction parseLocal(node: XmlNode): PseudopotentialLocal {\n return { vloc: parseData(textOf(node)) };\n}\n\nfunction parseBeta(node: XmlNode): BetaProjector {\n return {\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n angularMomentum: attrInt(node, \"angular_momentum\"),\n cutoffRadiusIndex: attr(node, \"cutoff_radius_index\")\n ? attrInt(node, \"cutoff_radius_index\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n normConservingRadius: attr(node, \"norm_conserving_radius\")\n ? attrNum(node, \"norm_conserving_radius\")\n : undefined,\n ultrasoftCutoffRadius: attrNum(node, \"ultrasoft_cutoff_radius\"),\n label: attr(node, \"label\"),\n beta: parseData(textOf(node)),\n };\n}\n\nfunction parseQijlKey(key: string): { i: number; j: number; l: number } \| null {\n const m = key.match(/^PP_QIJL\\.(\\d+)\\.(\\d+)\\.(\\d+)$/);\n if (!m) return null;\n return { i: parseIntSafe(m[1]), j: parseIntSafe(m[2]), l: parseIntSafe(m[3]) };\n}\n\nfunction parseAugmentation(node: XmlNode): AugmentationData {\n const qijl: QijlFunction[] = [];\n for (const [key, val] of entries(node)) {\n const ids = parseQijlKey(key);\n if (ids) {\n for (const q of toArray(val)) {\n qijl.push({ ...ids, qijl: parseData(textOf(q)) });\n }\n }\n }\n qijl.sort((a, b) => a.i - b.i \|\| a.j - b.j \|\| a.l - b.l);\n\n return {\n nqf: attr(node, \"nqf\") ? attrInt(node, \"nqf\") : undefined,\n nqlc: attr(node, \"nqlc\") ? attrInt(node, \"nqlc\") : undefined,\n qWithL: attr(node, \"q_with_l\") ? attrBool(node, \"q_with_l\") : undefined,\n shape: attr(node, \"shape\") \|\| undefined,\n rMatchAugfun: attr(node, \"r_match_augfun\")\n ? attrNum(node, \"r_match_augfun\")\n : undefined,\n cutoffR: attr(node, \"cutoff_r\")\n ? attrNum(node, \"cutoff_r\")\n : undefined,\n cutoffRIndex: attr(node, \"cutoff_r_index\")\n ? attrInt(node, \"cutoff_r_index\")\n : attr(node, \"iraug\")\n ? attrInt(node, \"iraug\")\n : undefined,\n irc: attr(node, \"irc\") ? attrInt(node, \"irc\") : undefined,\n lmaxAug: attr(node, \"l_max_aug\")\n ? attrInt(node, \"l_max_aug\")\n : attr(node, \"lmax_aug\")\n ? attrInt(node, \"lmax_aug\")\n : undefined,\n augmentationEpsilon: attr(node, \"augmentation_epsilon\")\n ? attrNum(node, \"augmentation_epsilon\")\n : undefined,\n q: node[\"PP_Q\"] ? parseData(textOf(node[\"PP_Q\"])) : undefined,\n multipoles: node[\"PP_MULTIPOLES\"]\n ? parseData(textOf(node[\"PP_MULTIPOLES\"]))\n : undefined,\n qfcoeff: node[\"PP_QFCOEFF\"]\n ? parseData(textOf(node[\"PP_QFCOEFF\"]))\n : undefined,\n rinner: node[\"PP_RINNER\"]\n ? parseData(textOf(node[\"PP_RINNER\"]))\n : undefined,\n qijl: qijl.length > 0 ? qijl : undefined,\n };\n}\n\nfunction parseNonlocal(node: XmlNode): PseudopotentialNonlocal {\n const betas: BetaProjector[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_BETA\" \|\| key.startsWith(\"PP_BETA.\")) {\n betas.push(...toArray(val).map(parseBeta));\n }\n }\n\n const dijText = textOf(node[\"PP_DIJ\"]);\n const tokens = dijText.trim().split(/\\s+/).filter(Boolean).map(parseFortranNumber);\n const dij: Array<[number, number, number]> = [];\n\n if (tokens.length > 0) {\n const nProj = betas.length;\n\n // Triplet format wins when every (nb, mb) pair is a plausible 1-based\n // projector index. This resolves the ambiguity where a triplet file\n // with nProj diagonal entries has exactly nProj^2 tokens (e.g. 3\n // projectors with 3 diagonal triplets = 9 tokens): a flat matrix of\n // floats is essentially never index-clean, while real triplets always\n // are.\n let tripletClean = false;\n if (nProj > 0 && tokens.length % 3 === 0) {\n tripletClean = true;\n for (let k = 0; k < tokens.length; k += 3) {\n const nb = tokens[k];\n const mb = tokens[k + 1];\n if (\n !Number.isInteger(nb) \|\|\n !Number.isInteger(mb) \|\|\n nb < 1 \|\|\n mb < 1 \|\|\n nb > nProj \|\|\n mb > nProj\n ) {\n tripletClean = false;\n break;\n }\n }\n }\n\n if (tripletClean) {\n for (let k = 0; k < tokens.length; k += 3) {\n dij.push([tokens[k], tokens[k + 1], tokens[k + 2]]);\n }\n }\n // Flat matrix format: tokens.length == nProj^2, row-major\n else if (nProj > 0 && tokens.length === nProj nProj) {\n for (let i = 0; i < nProj; i++) {\n for (let j = 0; j < nProj; j++) {\n dij.push([i + 1, j + 1, tokens[i * nProj + j]]);\n }\n }\n }\n // Lenient fallback: token count divisible by 3, parsed as triplets\n // even when the indices look out of range (legacy tolerance).\n else if (tokens.length % 3 === 0) {\n for (let k = 0; k < tokens.length; k += 3) {\n dij.push([tokens[k], tokens[k + 1], tokens[k + 2]]);\n }\n }\n }\n\n // PP_AUGMENTATION (optional, child of PP_NONLOCAL)\n const augmentation = node[\"PP_AUGMENTATION\"]\n ? parseAugmentation(node[\"PP_AUGMENTATION\"])\n : undefined;\n\n // nqf lives on the augmentation block; mirror it for convenience.\n const nqf = augmentation?.nqf ?? undefined;\n\n return { betas, dij, nqf, augmentation };\n}\n\nfunction parsePswfcNode(node: XmlNode): PseudopotentialWfc {\n return {\n l: attrInt(node, \"l\"),\n occupation: attrNum(node, \"occupation\"),\n label: attr(node, \"label\"),\n n: attr(node, \"n\") ? attrInt(node, \"n\") : undefined,\n pseudoEnergy: attr(node, \"pseudo_energy\")\n ? attrNum(node, \"pseudo_energy\")\n : undefined,\n cutoffRadius: attr(node, \"cutoff_radius\")\n ? attrNum(node, \"cutoff_radius\")\n : undefined,\n ultrasoftCutoffRadius: attr(node, \"ultrasoft_cutoff_radius\")\n ? attrNum(node, \"ultrasoft_cutoff_radius\")\n : undefined,\n chi: parseData(textOf(node)),\n };\n}\n\nfunction parseFullWfcNode(node: XmlNode): FullWfc {\n return {\n l: attrInt(node, \"l\"),\n label: attr(node, \"label\"),\n aewfc: parseData(textOf(node)),\n };\n}\n\n/** Parse PP_PAW, including any non-standard PP_AEWFC/PP_PSWFC children. /\nfunction parsePaw(node: XmlNode): PawData {\n const innerAeWfcs: FullWfc[] = [];\n const innerPsWfcs: FullWfc[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_AEWFC\" \|\| key.startsWith(\"PP_AEWFC.\")) {\n for (const wfc of toArray(val)) innerAeWfcs.push(parseFullWfcNode(wfc));\n }\n if (key === \"PP_PSWFC\" \|\| key.startsWith(\"PP_PSWFC.\")) {\n for (const wfc of toArray(val)) innerPsWfcs.push(parseFullWfcNode(wfc));\n }\n }\n return {\n pawDataFormat: attrInt(node, \"paw_data_format\"),\n coreEnergy: attrNum(node, \"core_energy\"),\n occupations: node[\"PP_OCCUPATIONS\"]\n ? parseData(textOf(node[\"PP_OCCUPATIONS\"]))\n : new Float64Array(0),\n aeNlcc: node[\"PP_AE_NLCC\"]\n ? parseData(textOf(node[\"PP_AE_NLCC\"]))\n : new Float64Array(0),\n aeVloc: node[\"PP_AE_VLOC\"]\n ? parseData(textOf(node[\"PP_AE_VLOC\"]))\n : new Float64Array(0),\n aeWfcs: innerAeWfcs,\n psWfcs: innerPsWfcs,\n };\n}\n\nfunction parseGipaw(\n node: XmlNode,\n tag: \"PP_GIPAW\" \| \"PP_GIPAW_RECONSTRUCTION\",\n): GipawData {\n const coreOrbitals: GipawData[\"coreOrbitals\"] = [];\n const coreOrbsSection = node[\"PP_GIPAW_CORE_ORBITALS\"];\n if (coreOrbsSection) {\n for (const [key, val] of entries(coreOrbsSection)) {\n if (key.startsWith(\"PP_GIPAW_CORE_ORBITAL.\")) {\n for (const co of toArray(val)) {\n coreOrbitals.push({\n n: attrInt(co, \"n\"),\n l: attrInt(co, \"l\"),\n orbital: parseData(textOf(co)),\n });\n }\n }\n }\n }\n\n const orbitals: GipawData[\"orbitals\"] = [];\n const orbsSection = node[\"PP_GIPAW_ORBITALS\"];\n if (orbsSection) {\n for (const [key, val] of entries(orbsSection)) {\n if (key.startsWith(\"PP_GIPAW_ORBITAL.\")) {\n for (const orb of toArray(val)) {\n orbitals.push({\n l: attrInt(orb, \"l\"),\n label: attr(orb, \"label\"),\n aeOrbital: orb[\"PP_GIPAW_ORBITAL_AE\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_AE\"]))\n : new Float64Array(0),\n psOrbital: orb[\"PP_GIPAW_ORBITAL_PS\"]\n ? parseData(textOf(orb[\"PP_GIPAW_ORBITAL_PS\"]))\n : new Float64Array(0),\n });\n }\n }\n }\n }\n\n let vlocAe: Float64Array = new Float64Array(0);\n let vlocPs: Float64Array = new Float64Array(0);\n const vlocalSection = node[\"PP_GIPAW_VLOCAL\"];\n if (vlocalSection) {\n vlocAe = vlocalSection[\"GIPAW_VLOCAL_AE\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_AE\"]))\n : vlocAe;\n vlocPs = vlocalSection[\"GIPAW_VLOCAL_PS\"]\n ? parseData(textOf(vlocalSection[\"GIPAW_VLOCAL_PS\"]))\n : vlocPs;\n }\n\n return {\n tag,\n gipawDataFormat: attrInt(node, \"gipaw_data_format\"),\n coreOrbitals,\n orbitals,\n vlocAe,\n vlocPs,\n };\n}\n\nfunction parseRelWfc(node: XmlNode): RelativisticWfc {\n return {\n jchi: attrNum(node, \"jchi\"),\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n els: attr(node, \"els\") \|\| undefined,\n nn: attr(node, \"nn\") ? attrInt(node, \"nn\") : undefined,\n lchi: attr(node, \"lchi\") ? attrInt(node, \"lchi\") : undefined,\n oc: attr(node, \"oc\") ? attrNum(node, \"oc\") : undefined,\n chi: parseOptionalData(textOf(node)),\n };\n}\n\nfunction parseRelBeta(node: XmlNode): RelativisticBeta {\n return {\n jjj: attrNum(node, \"jjj\"),\n index: attr(node, \"index\") ? attrInt(node, \"index\") : undefined,\n lll: attr(node, \"lll\") ? attrInt(node, \"lll\") : undefined,\n beta: parseOptionalData(textOf(node)),\n };\n}\n\nfunction parseSpinOrbit(node: XmlNode): SpinOrbitData {\n const relWfcs: RelativisticWfc[] = [];\n const relBetas: RelativisticBeta[] = [];\n for (const [key, val] of entries(node)) {\n if (key === \"PP_RELWFC\" \|\| key.startsWith(\"PP_RELWFC.\")) {\n for (const wfc of toArray(val)) relWfcs.push(parseRelWfc(wfc));\n }\n if (key === \"PP_RELBETA\" \|\| key.startsWith(\"PP_RELBETA.\")) {\n for (const beta of toArray(val)) relBetas.push(parseRelBeta(beta));\n }\n }\n return { relWfcs, relBetas };\n}\n\n/* Extract raw PP_INPUTFILE content (may hold non-XML generator input). /\nfunction extractInputFile(text: string): string \| undefined {\n const m = text.match(/<PP_INPUTFILE>([\\s\\S]?)<\\/PP_INPUTFILE>/);\n if (!m) return undefined;\n const content = m[1].trim();\n return content \|\| undefined;\n}\n\n// ── Main parser ────────────────────────────────────────────────────\n\n/*\n Parse a UPF v2.0.1 pseudopotential string into a first-class\n * Pseudopotential object.\n \n @param text - The complete UPF file content as a string.\n * @returns A parsed Pseudopotential object.\n * @throws If the text is not valid UPF v2.0.1 format.\n /\nexport function fromUPF(text: string): Pseudopotential {\n const doc = parseXml(text);\n\n const upf: XmlNode = doc?.UPF;\n if (!upf) {\n throw new Error(\"Not a UPF file: missing <UPF> root element\");\n }\n\n const version = ((attr(upf, \"version\") \|\| \"2.0.1\") as UPFVersion);\n\n // PP_INFO (optional, plain text)\n const info = upf[\"PP_INFO\"] ? textOf(upf[\"PP_INFO\"]).trim() \|\| undefined : undefined;\n\n // PP_INPUTFILE (optional, raw text — may contain generator input)\n const inputFile = extractInputFile(text);\n\n // PP_HEADER (required, self-closing tag with attributes)\n if (!upf[\"PP_HEADER\"]) {\n throw new Error(\"Missing PP_HEADER section\");\n }\n const header = parseHeader(upf[\"PP_HEADER\"]);\n\n // PP_MESH (required)\n if (!upf[\"PP_MESH\"]) {\n throw new Error(\"Missing PP_MESH section\");\n }\n const mesh = parseMesh(upf[\"PP_MESH\"]);\n\n // PP_NLCC (optional)\n const nlcc = upf[\"PP_NLCC\"] ? parseData(textOf(upf[\"PP_NLCC\"])) : undefined;\n\n // PP_LOCAL (required)\n if (!upf[\"PP_LOCAL\"]) {\n throw new Error(\"Missing PP_LOCAL section\");\n }\n const local = parseLocal(upf[\"PP_LOCAL\"]);\n\n // PP_SEMILOCAL (optional)\n let semilocal: Pseudopotential[\"semilocal\"] \| undefined;\n if (upf[\"PP_SEMILOCAL\"]) {\n semilocal = toArray<XmlNode>(upf[\"PP_SEMILOCAL\"][\"PP_VNL\"]).map((vnl: XmlNode) => ({\n l: attrInt(vnl, \"L\"),\n j: attr(vnl, \"J\") ? attrNum(vnl, \"J\") : undefined,\n vnl: parseData(textOf(vnl)),\n }));\n }\n\n // PP_NONLOCAL (required)\n if (!upf[\"PP_NONLOCAL\"]) {\n throw new Error(\"Missing PP_NONLOCAL section\");\n }\n const nonlocal = parseNonlocal(upf[\"PP_NONLOCAL\"]);\n\n // PP_PSWFC (optional)\n const pswfcRaw = upf[\"PP_PSWFC\"];\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcRaw) {\n for (const [key, val] of entries(pswfcRaw)) {\n if (key === \"PP_CHI\" \|\| key.startsWith(\"PP_CHI.\")) {\n for (const chi of toArray(val)) {\n pswfc.push(parsePswfcNode(chi));\n }\n }\n }\n }\n\n // PP_FULL_WFC (optional, PAW only)\n let fullWfc: FullWfc[] \| undefined;\n if (upf[\"PP_FULL_WFC\"]) {\n const wfcs: FullWfc[] = [];\n for (const [key, val] of entries(upf[\"PP_FULL_WFC\"])) {\n if (key === \"PP_AEWFC\" \|\| key.startsWith(\"PP_AEWFC\")) {\n for (const wfc of toArray(val)) {\n wfcs.push(parseFullWfcNode(wfc));\n }\n }\n }\n fullWfc = wfcs.length > 0 ? wfcs : undefined;\n }\n\n // PP_RHOATOM (required)\n if (!upf[\"PP_RHOATOM\"]) {\n throw new Error(\"Missing PP_RHOATOM section\");\n }\n const rhoatom = parseData(textOf(upf[\"PP_RHOATOM\"]));\n\n // PP_PAW (optional)\n const paw = upf[\"PP_PAW\"] ? parsePaw(upf[\"PP_PAW\"]) : undefined;\n\n // PP_GIPAW (optional — tag may be PP_GIPAW or PP_GIPAW_RECONSTRUCTION)\n const gipaw = upf[\"PP_GIPAW\"]\n ? parseGipaw(upf[\"PP_GIPAW\"], \"PP_GIPAW\")\n : upf[\"PP_GIPAW_RECONSTRUCTION\"]\n ? parseGipaw(upf[\"PP_GIPAW_RECONSTRUCTION\"], \"PP_GIPAW_RECONSTRUCTION\")\n : undefined;\n\n // PP_SPIN_ORB (optional)\n const spinOrbit = upf[\"PP_SPIN_ORB\"]\n ? parseSpinOrbit(upf[\"PP_SPIN_ORB\"])\n : undefined;\n\n // Merge any non-standard inner PAW wavefunctions into the top-level lists\n // (UPF v2.0.1 spec keeps PP_FULL_WFC / PP_PSWFC as siblings of PP_PAW, but\n // some generators nest PP_AEWFC / PP_PSWFC inside PP_PAW).\n if (paw) {\n if (paw.aeWfcs.length > 0) {\n fullWfc = [...(fullWfc ?? []), ...paw.aeWfcs];\n }\n if (paw.psWfcs.length > 0 && pswfc.length === 0) {\n for (const w of paw.psWfcs) {\n pswfc.push({ l: w.l, occupation: 0, label: w.label, chi: w.aewfc });\n }\n }\n paw.aeWfcs = fullWfc ?? [];\n paw.psWfcs =\n paw.psWfcs.length > 0\n ? paw.psWfcs\n : pswfc.map((w) => ({\n l: w.l,\n label: w.label ?? \"\",\n aewfc: w.chi,\n }));\n }\n\n return {\n format: \"UPF2\",\n version,\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"UPF2\" },\n info,\n inputFile,\n header,\n mesh,\n nlcc,\n local,\n semilocal,\n nonlocal,\n pswfc,\n fullWfc,\n rhoatom,\n paw,\n gipaw,\n spinOrbit,\n };\n}\n\n// ── Serializer ─────────────────────────────────────────────────────\n\n/\n Serialize a first-class Pseudopotential object back to UPF v2.0.1 format.\n \n @param pp - The pseudopotential to serialize.\n * @returns The UPF file content as a string.\n /\nexport function toUPF(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n lines.push(`<UPF version=\"${pp.version ?? \"2.0.1\"}\">`);\n lines.push(\"\");\n\n // PP_INFO\n if (pp.info) {\n lines.push(\"<PP_INFO>\");\n lines.push(pp.info);\n lines.push(\"</PP_INFO>\");\n lines.push(\"\");\n }\n\n // PP_HEADER: header fields take precedence; provenance creator/date fill\n // in for objects arriving from formats without header equivalents (PSML,\n // FHI), so generator stamps survive a hub conversion.\n lines.push(\"<PP_HEADER\");\n lines.push(` generated=\"${escapeXmlAttr(pp.header.generated ?? pp.provenance.creator ?? \"\")}\"`);\n lines.push(` author=\"${escapeXmlAttr(pp.header.author ?? \"\")}\"`);\n lines.push(` date=\"${escapeXmlAttr(pp.header.date ?? pp.provenance.date ?? \"\")}\"`);\n lines.push(` comment=\"${escapeXmlAttr(pp.header.comment ?? \"\")}\"`);\n lines.push(` element=\"${pp.header.element}\"`);\n lines.push(` pseudo_type=\"${pp.header.pseudoType}\"`);\n lines.push(` relativistic=\"${pp.header.relativistic}\"`);\n lines.push(` is_ultrasoft=\"${formatFortranBool(pp.header.isUltrasoft)}\"`);\n lines.push(` is_paw=\"${formatFortranBool(pp.header.isPaw)}\"`);\n lines.push(` is_coulomb=\"${formatFortranBool(pp.header.isCoulomb)}\"`);\n lines.push(` has_so=\"${formatFortranBool(pp.header.hasSo)}\"`);\n lines.push(` has_wfc=\"${formatFortranBool(pp.header.hasWfc)}\"`);\n lines.push(` has_gipaw=\"${formatFortranBool(pp.header.hasGipaw)}\"`);\n lines.push(` paw_as_gipaw=\"${formatFortranBool(pp.header.pawAsGipaw)}\"`);\n lines.push(` core_correction=\"${formatFortranBool(pp.header.coreCorrection)}\"`);\n lines.push(` functional=\"${pp.header.functional}\"`);\n lines.push(` z_valence=\"${formatFortranNumber(pp.header.zValence)}\"`);\n lines.push(` total_psenergy=\"${formatFortranNumber(pp.header.totalPsenergy)}\"`);\n lines.push(` wfc_cutoff=\"${formatFortranNumber(pp.header.wfcCutoff)}\"`);\n lines.push(` rho_cutoff=\"${formatFortranNumber(pp.header.rhoCutoff)}\"`);\n lines.push(` l_max=\"${pp.header.lMax}\"`);\n lines.push(` l_max_rho=\"${pp.header.lMaxRho}\"`);\n lines.push(` l_local=\"${pp.header.lLocal}\"`);\n lines.push(` mesh_size=\"${pp.header.meshSize}\"`);\n lines.push(` number_of_wfc=\"${pp.header.numberOfWfc}\"`);\n lines.push(` number_of_proj=\"${pp.header.numberOfProj}\"/>`);\n lines.push(\"\");\n\n // PP_MESH\n const meshAttrs: string[] = [];\n if (pp.mesh.dx != null) meshAttrs.push(`dx=\"${pp.mesh.dx}\"`);\n if (pp.mesh.mesh != null) meshAttrs.push(`mesh=\"${pp.mesh.mesh}\"`);\n if (pp.mesh.xmin != null) meshAttrs.push(`xmin=\"${pp.mesh.xmin}\"`);\n meshAttrs.push(`rmax=\"${pp.mesh.rmax}\"`);\n if (pp.mesh.zmesh != null) meshAttrs.push(`zmesh=\"${pp.mesh.zmesh}\"`);\n lines.push(`<PP_MESH ${meshAttrs.join(\" \")}>`);\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n lines.push(\"\");\n\n // PP_NLCC (optional)\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n lines.push(\"\");\n }\n\n // PP_LOCAL\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n lines.push(\"\");\n\n // PP_SEMILOCAL (optional)\n if (pp.semilocal) {\n lines.push(\"<PP_SEMILOCAL>\");\n for (const vnl of pp.semilocal) {\n lines.push(`<PP_VNL L=\"${vnl.l}\"${vnl.j !== undefined ? ` J=\"${vnl.j}\"` : \"\"}>`);\n lines.push(formatDataArray(vnl.vnl));\n lines.push(\"</PP_VNL>\");\n }\n lines.push(\"</PP_SEMILOCAL>\");\n lines.push(\"\");\n }\n\n // PP_NONLOCAL\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n const betaAttrs = [\n `angular_momentum=\"${beta.angularMomentum}\"`,\n `label=\"${beta.label}\"`,\n ];\n // Preserve document order without inventing attributes: only write\n // index when the source carried one.\n if (beta.index != null) betaAttrs.unshift(`index=\"${beta.index}\"`);\n if (beta.cutoffRadiusIndex != null) betaAttrs.push(`cutoff_radius_index=\"${beta.cutoffRadiusIndex}\"`);\n if (beta.cutoffRadius != null) betaAttrs.push(`cutoff_radius=\"${formatFortranNumber(beta.cutoffRadius)}\"`);\n if (beta.normConservingRadius != null) betaAttrs.push(`norm_conserving_radius=\"${formatFortranNumber(beta.normConservingRadius)}\"`);\n betaAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(beta.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_BETA ${betaAttrs.join(\" \")}>`);\n lines.push(formatDataArray(beta.beta));\n lines.push(\"</PP_BETA>\");\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(`${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n\n // PP_AUGMENTATION (optional, USPP/PAW)\n if (pp.nonlocal.augmentation) {\n const aug = pp.nonlocal.augmentation;\n const augAttrs: string[] = [];\n if (aug.qWithL != null) augAttrs.push(`q_with_l=\"${aug.qWithL ? \"T\" : \"F\"}\"`);\n if (aug.nqf != null) augAttrs.push(`nqf=\"${aug.nqf}\"`);\n if (aug.nqlc != null) augAttrs.push(`nqlc=\"${aug.nqlc}\"`);\n if (aug.shape != null) augAttrs.push(`shape=\"${aug.shape}\"`);\n if (aug.rMatchAugfun != null) augAttrs.push(`r_match_augfun=\"${formatFortranNumber(aug.rMatchAugfun)}\"`);\n if (aug.cutoffR != null) augAttrs.push(`cutoff_r=\"${formatFortranNumber(aug.cutoffR)}\"`);\n if (aug.cutoffRIndex != null) augAttrs.push(`cutoff_r_index=\"${aug.cutoffRIndex}\"`);\n if (aug.irc != null) augAttrs.push(`irc=\"${aug.irc}\"`);\n if (aug.lmaxAug != null) augAttrs.push(`l_max_aug=\"${aug.lmaxAug}\"`);\n if (aug.augmentationEpsilon != null) augAttrs.push(`augmentation_epsilon=\"${formatFortranNumber(aug.augmentationEpsilon)}\"`);\n lines.push(`<PP_AUGMENTATION ${augAttrs.join(\" \")}>`);\n if (aug.q) {\n lines.push(\"<PP_Q>\");\n lines.push(formatDataArray(aug.q));\n lines.push(\"</PP_Q>\");\n }\n if (aug.multipoles) {\n lines.push(\"<PP_MULTIPOLES>\");\n lines.push(formatDataArray(aug.multipoles));\n lines.push(\"</PP_MULTIPOLES>\");\n }\n if (aug.qfcoeff) {\n lines.push(\"<PP_QFCOEFF>\");\n lines.push(formatDataArray(aug.qfcoeff));\n lines.push(\"</PP_QFCOEFF>\");\n }\n if (aug.rinner) {\n lines.push(\"<PP_RINNER>\");\n lines.push(formatDataArray(aug.rinner));\n lines.push(\"</PP_RINNER>\");\n }\n if (aug.qijl) {\n for (const q of aug.qijl) {\n lines.push(`<PP_QIJL.${q.i}.${q.j}.${q.l}>`);\n lines.push(formatDataArray(q.qijl));\n lines.push(`</PP_QIJL.${q.i}.${q.j}.${q.l}>`);\n }\n }\n lines.push(\"</PP_AUGMENTATION>\");\n }\n\n lines.push(\"</PP_NONLOCAL>\");\n lines.push(\"\");\n\n // PP_PSWFC\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (let i = 0; i < pp.pswfc.length; i++) {\n const wfc = pp.pswfc[i];\n const chiAttrs = [\n `index=\"${i + 1}\"`,\n `l=\"${wfc.l}\"`,\n `occupation=\"${formatFortranNumber(wfc.occupation)}\"`,\n `label=\"${wfc.label ?? \"\"}\"`,\n ];\n if (wfc.n != null) chiAttrs.push(`n=\"${wfc.n}\"`);\n if (wfc.pseudoEnergy != null) chiAttrs.push(`pseudo_energy=\"${formatFortranNumber(wfc.pseudoEnergy)}\"`);\n if (wfc.cutoffRadius != null) chiAttrs.push(`cutoff_radius=\"${formatFortranNumber(wfc.cutoffRadius)}\"`);\n if (wfc.ultrasoftCutoffRadius != null) chiAttrs.push(`ultrasoft_cutoff_radius=\"${formatFortranNumber(wfc.ultrasoftCutoffRadius)}\"`);\n lines.push(`<PP_CHI ${chiAttrs.join(\" \")}>`);\n lines.push(formatDataArray(wfc.chi));\n lines.push(\"</PP_CHI>\");\n }\n lines.push(\"</PP_PSWFC>\");\n lines.push(\"\");\n }\n\n // PP_FULL_WFC (optional)\n if (pp.fullWfc && pp.fullWfc.length > 0) {\n lines.push(\"<PP_FULL_WFC>\");\n for (const wfc of pp.fullWfc) {\n lines.push(`<PP_AEWFC l=\"${wfc.l}\" label=\"${wfc.label}\">`);\n lines.push(formatDataArray(wfc.aewfc));\n lines.push(\"</PP_AEWFC>\");\n }\n lines.push(\"</PP_FULL_WFC>\");\n lines.push(\"\");\n }\n\n // PP_RHOATOM\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n lines.push(\"\");\n\n // PP_PAW (optional): block holds OCCUPATIONS / AE_NLCC / AE_VLOC only;\n // wavefunctions live in the top-level PP_PSWFC / PP_FULL_WFC sections.\n if (pp.paw) {\n lines.push(`<PP_PAW paw_data_format=\"${pp.paw.pawDataFormat}\" core_energy=\"${formatFortranNumber(pp.paw.coreEnergy)}\">`);\n if (pp.paw.occupations.length > 0) {\n lines.push(\"<PP_OCCUPATIONS>\");\n lines.push(formatDataArray(pp.paw.occupations));\n lines.push(\"</PP_OCCUPATIONS>\");\n }\n if (pp.paw.aeNlcc.length > 0) {\n lines.push(\"<PP_AE_NLCC>\");\n lines.push(formatDataArray(pp.paw.aeNlcc));\n lines.push(\"</PP_AE_NLCC>\");\n }\n if (pp.paw.aeVloc.length > 0) {\n lines.push(\"<PP_AE_VLOC>\");\n lines.push(formatDataArray(pp.paw.aeVloc));\n lines.push(\"</PP_AE_VLOC>\");\n }\n lines.push(\"</PP_PAW>\");\n lines.push(\"\");\n }\n\n // PP_GIPAW (optional): preserve the original tag variant.\n if (pp.gipaw) {\n const tag = pp.gipaw.tag ?? \"PP_GIPAW\";\n lines.push(`<${tag} gipaw_data_format=\"${pp.gipaw.gipawDataFormat}\">`);\n if (pp.gipaw.coreOrbitals.length > 0) {\n lines.push(`<PP_GIPAW_CORE_ORBITALS number_of_core_orbitals=\"${pp.gipaw.coreOrbitals.length}\">`);\n for (let i = 0; i < pp.gipaw.coreOrbitals.length; i++) {\n const co = pp.gipaw.coreOrbitals[i];\n lines.push(`<PP_GIPAW_CORE_ORBITAL.${i + 1} n=\"${co.n}\" l=\"${co.l}\">`);\n if (co.orbital.length > 0) lines.push(formatDataArray(co.orbital));\n lines.push(`</PP_GIPAW_CORE_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_CORE_ORBITALS>\");\n }\n if (pp.gipaw.orbitals.length > 0) {\n lines.push(\"<PP_GIPAW_ORBITALS>\");\n for (let i = 0; i < pp.gipaw.orbitals.length; i++) {\n const orb = pp.gipaw.orbitals[i];\n lines.push(`<PP_GIPAW_ORBITAL.${i + 1} l=\"${orb.l}\" label=\"${escapeXmlAttr(orb.label)}\">`);\n lines.push(\"<PP_GIPAW_ORBITAL_AE>\");\n lines.push(formatDataArray(orb.aeOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_AE>\");\n lines.push(\"<PP_GIPAW_ORBITAL_PS>\");\n lines.push(formatDataArray(orb.psOrbital));\n lines.push(\"</PP_GIPAW_ORBITAL_PS>\");\n lines.push(`</PP_GIPAW_ORBITAL.${i + 1}>`);\n }\n lines.push(\"</PP_GIPAW_ORBITALS>\");\n }\n if (pp.gipaw.vlocAe.length > 0 \|\| pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<PP_GIPAW_VLOCAL>\");\n if (pp.gipaw.vlocAe.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_AE>\");\n lines.push(formatDataArray(pp.gipaw.vlocAe));\n lines.push(\"</GIPAW_VLOCAL_AE>\");\n }\n if (pp.gipaw.vlocPs.length > 0) {\n lines.push(\"<GIPAW_VLOCAL_PS>\");\n lines.push(formatDataArray(pp.gipaw.vlocPs));\n lines.push(\"</GIPAW_VLOCAL_PS>\");\n }\n lines.push(\"</PP_GIPAW_VLOCAL>\");\n }\n lines.push(`</${tag}>`);\n lines.push(\"\");\n }\n\n // PP_SPIN_ORB (optional)\n if (pp.spinOrbit) {\n lines.push(\"<PP_SPIN_ORB>\");\n let relIdx = 1;\n for (const wfc of pp.spinOrbit.relWfcs) {\n const attrs = [\n `index=\"${wfc.index ?? relIdx}\"`,\n `jchi=\"${formatFortranNumber(wfc.jchi)}\"`,\n ];\n if (wfc.els != null) attrs.push(`els=\"${escapeXmlAttr(wfc.els)}\"`);\n if (wfc.nn != null) attrs.push(`nn=\"${wfc.nn}\"`);\n if (wfc.lchi != null) attrs.push(`lchi=\"${wfc.lchi}\"`);\n if (wfc.oc != null) attrs.push(`oc=\"${formatFortranNumber(wfc.oc)}\"`);\n lines.push(`<PP_RELWFC ${attrs.join(\" \")}>`);\n if (wfc.chi && wfc.chi.length > 0) lines.push(formatDataArray(wfc.chi));\n lines.push(\"</PP_RELWFC>\");\n relIdx++;\n }\n let betaIdx = 1;\n for (const beta of pp.spinOrbit.relBetas) {\n const attrs = [\n `index=\"${beta.index ?? betaIdx}\"`,\n `jjj=\"${formatFortranNumber(beta.jjj)}\"`,\n ];\n if (beta.lll != null) attrs.push(`lll=\"${beta.lll}\"`);\n lines.push(`<PP_RELBETA ${attrs.join(\" \")}>`);\n if (beta.beta && beta.beta.length > 0) lines.push(formatDataArray(beta.beta));\n lines.push(\"</PP_RELBETA>\");\n betaIdx++;\n }\n lines.push(\"</PP_SPIN_ORB>\");\n lines.push(\"\");\n }\n\n // PP_INPUTFILE (optional, verbatim)\n if (pp.inputFile) {\n lines.push(\"<PP_INPUTFILE>\");\n lines.push(pp.inputFile);\n lines.push(\"</PP_INPUTFILE>\");\n lines.push(\"\");\n }\n\n lines.push(\"</UPF>\");\n\n return lines.join(\"\\n\");\n}\n","/\n UPF v1 pseudopotential parser and serializer.\n \n UPF v1 is the legacy Quantum ESPRESSO format with fixed-width headers\n * and `<SECTION>`/`</SECTION>` delimiters (not XML attributes).\n * Units: Rydberg (energy), Bohr (length) — same as UPF v2.\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nfunction extractSection(text: string, tag: string): string \| null {\n const open = `<${tag}>`;\n const close = `</${tag}>`;\n const start = text.indexOf(open);\n if (start === -1) return null;\n const end = text.indexOf(close, start);\n if (end === -1) return null;\n return text.substring(start + open.length, end);\n}\n\nfunction extractSubSection(text: string, tag: string): string \| null {\n return extractSection(text, tag);\n}\n\nfunction lines(text: string): string[] {\n return text.split(\"\\n\").filter((l) => l.trim().length > 0);\n}\n\n/\n Parse a UPF v1 pseudopotential string.\n \n UPF v1 format:\n * - First line: version number (0 or 1)\n * - Header: element, type, functional, z_valence, etc.\n * - `<PP_MESH>`: radial grid\n * - `<PP_LOCAL>`: local potential\n * - `<PP_NONLOCAL>`: projectors and D_ij\n * - `<PP_PSWFC>`: pseudo wavefunctions\n * - `<PP_RHOATOM>`: atomic charge density\n /\nexport function fromUPFv1(text: string): Pseudopotential {\n // Detect UPF v1: first non-empty line should be a number\n const firstLine = text.trim().split(\"\\n\")[0].trim();\n const versionMatch = firstLine.match(/^(\\d+)/);\n if (!versionMatch) {\n throw new Error(\"Not a UPF v1 file: first line is not a version number\");\n }\n\n // Extract header section\n const headerSection = extractSection(text, \"PP_HEADER\");\n if (!headerSection) throw new Error(\"Missing PP_HEADER section\");\n\n const headerLines = lines(headerSection);\n\n // Parse header fields (UPF v1 uses free-format Fortran reads)\n // Line format varies; we parse what we can find\n let element = \"X\";\n let pseudoType: PseudopotentialHeader[\"pseudoType\"] = \"NC\";\n let functional = \"\";\n let zValence = 0;\n let lMax = 0;\n let meshSize = 0;\n let numberOfWfc = 0;\n let numberOfProj = 0;\n let coreCorrection = false;\n\n for (const line of headerLines) {\n const trimmed = line.trim();\n // Try to extract element from first meaningful line\n // Handle quoted element names like 'H' or unquoted like H\n const elemMatch = trimmed.match(/^['\"]?([A-Z][a-z]?)['\"]?(?:\\s\|$)/);\n if (elemMatch) {\n element = elemMatch[1];\n }\n // Look for pseudo type indicators\n if (trimmed.includes(\"'NC'\") \|\| trimmed.includes('\"NC\"') \|\| trimmed.includes(\"NC\")) {\n pseudoType = \"NC\";\n }\n if (trimmed.includes(\"'US'\") \|\| trimmed.includes('\"US\"') \|\| trimmed.includes(\"US\")) {\n pseudoType = \"US\";\n }\n if (trimmed.includes(\"'PAW'\") \|\| trimmed.includes('\"PAW\"') \|\| trimmed.includes(\"PAW\")) {\n pseudoType = \"PAW\";\n }\n // Look for functional (quoted string like 'SLA-PW-PBE-PBE')\n const funcMatch = trimmed.match(/^['\"]([^'\"]+)['\"]/);\n if (funcMatch && (funcMatch[1].includes(\"SLA\") \|\| funcMatch[1].includes(\"PBE\") \|\| funcMatch[1].includes(\"LDA\"))) {\n functional = funcMatch[1];\n }\n // Look for z_valence\n const zMatch = trimmed.match(/(\\d+\\.?\\d)\\s(?:zp\|z_valence\|z_p)/i);\n if (zMatch) zValence = parseFloat(zMatch[1]);\n // Look for lmax\n const lmaxMatch = trimmed.match(/lmax\\s=\\s(\\d+)/i);\n if (lmaxMatch) lMax = parseInt(lmaxMatch[1]);\n // Look for mesh size\n const meshMatch = trimmed.match(/mesh\\s=\\s(\\d+)/i);\n if (meshMatch) meshSize = parseInt(meshMatch[1]);\n // Look for number of wavefunctions and projectors\n const nwfcMatch = trimmed.match(/(\\d+)\\s+(\\d+)\\s+(?:nwfc\|nbeta)/i);\n if (nwfcMatch) {\n numberOfWfc = parseInt(nwfcMatch[1]);\n numberOfProj = parseInt(nwfcMatch[2]);\n }\n // Core correction\n if (trimmed.includes(\".true.\") \|\| trimmed.includes(\"T\")) {\n coreCorrection = true;\n }\n }\n\n // Parse PP_MESH section\n const meshSection = extractSection(text, \"PP_MESH\");\n let r: Float64Array = new Float64Array(0);\n let rab: Float64Array = new Float64Array(0);\n\n if (meshSection) {\n const rSection = extractSubSection(meshSection, \"PP_R\");\n const rabSection = extractSubSection(meshSection, \"PP_RAB\");\n if (rSection) r = parseFloat64Array(rSection);\n if (rabSection) rab = parseFloat64Array(rabSection);\n }\n\n if (r.length === 0) throw new Error(\"Empty or missing PP_R section\");\n meshSize = r.length;\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Parse PP_LOCAL section\n const localSection = extractSection(text, \"PP_LOCAL\");\n if (!localSection) throw new Error(\"Missing PP_LOCAL section\");\n const local: PseudopotentialLocal = { vloc: parseFloat64Array(localSection) };\n\n // Parse PP_NONLOCAL section\n const nonlocalSection = extractSection(text, \"PP_NONLOCAL\");\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n\n if (nonlocalSection) {\n // Parse beta projectors\n const betaMatches = nonlocalSection.match(/<PP_BETA[^>]>([\\s\\S]?)<\\/PP_BETA>/g);\n if (betaMatches) {\n for (const betaBlock of betaMatches) {\n const inner = betaBlock.replace(/<\\/?PP_BETA[^>]>/g, \"\");\n const innerLines = lines(inner);\n if (innerLines.length >= 2) {\n // First line: nbeta, lll, label\n const metaParts = innerLines[0].trim().split(/\\s+/);\n const l = metaParts.length >= 2 ? parseInt(metaParts[1]) : 0;\n const label = metaParts.length >= 3 ? metaParts[2].replace(/['\"]/g, \"\") : `l=${l}`;\n\n // Second line: kkbeta (cutoff index)\n const cutoffLine = innerLines[1].trim().split(/\\s+/);\n const cutoffIndex = cutoffLine.length >= 1 ? parseInt(cutoffLine[0]) : 0;\n\n // Remaining lines: projector data\n const dataText = innerLines.slice(1).join(\"\\n\");\n const betaData = parseFloat64Array(dataText.replace(/^\\s\\d+\\s+/gm, \"\"));\n\n betas.push({\n angularMomentum: l,\n cutoffRadiusIndex: cutoffIndex,\n ultrasoftCutoffRadius: 0,\n label,\n beta: betaData,\n });\n }\n }\n }\n\n // Parse D_ij\n const dijSection = extractSection(nonlocalSection, \"PP_DIJ\");\n if (dijSection) {\n const dijLines = lines(dijSection);\n for (const line of dijLines) {\n const parts = line.trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 3) {\n const nb = parseInt(parts[0]);\n const mb = parseInt(parts[1]);\n const val = parseFortranNumber(parts[2]);\n if (!isNaN(nb) && !isNaN(mb) && !isNaN(val)) {\n dij.push([nb, mb, val]);\n }\n }\n }\n }\n }\n\n const nonlocal: PseudopotentialNonlocal = { betas, dij };\n\n // Parse PP_PSWFC section\n const pswfcSection = extractSection(text, \"PP_PSWFC\");\n const pswfc: PseudopotentialWfc[] = [];\n\n if (pswfcSection) {\n const pswfcLines = lines(pswfcSection);\n let i = 0;\n while (i < pswfcLines.length) {\n const line = pswfcLines[i].trim();\n // Wavefunction header: label l oc\n const wfcMatch = line.match(/['\"]?(\\w+)['\"]?\\s+(\\d+)\\s+([\\d.]+)/);\n if (wfcMatch) {\n const label = wfcMatch[1];\n const l = parseInt(wfcMatch[2]);\n const occupation = parseFloat(wfcMatch[3]);\n i++;\n // Collect data lines until next header or end\n const dataLines: string[] = [];\n while (i < pswfcLines.length && !pswfcLines[i].trim().match(/['\"]?\\w+['\"]?\\s+\\d+\\s+[\\d.]+/)) {\n dataLines.push(pswfcLines[i]);\n i++;\n }\n const chi = parseFloat64Array(dataLines.join(\"\\n\"));\n pswfc.push({ l, occupation, label, chi });\n } else {\n i++;\n }\n }\n }\n\n // Parse PP_NLCC section (optional)\n const nlccSection = extractSection(text, \"PP_NLCC\");\n const nlcc = nlccSection ? parseFloat64Array(nlccSection) : undefined;\n\n // Parse PP_RHOATOM section\n const rhoatomSection = extractSection(text, \"PP_RHOATOM\");\n const rhoatom = rhoatomSection ? parseFloat64Array(rhoatomSection) : new Float64Array(meshSize);\n\n return {\n format: \"UPF1\",\n version: \"1.0.0\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"UPF1\" },\n header: {\n element,\n pseudoType,\n relativistic: \"scalar\",\n isUltrasoft: pseudoType === \"US\",\n isPaw: pseudoType === \"PAW\",\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize,\n numberOfWfc,\n numberOfProj,\n },\n mesh,\n nlcc,\n local,\n nonlocal,\n pswfc,\n rhoatom,\n };\n}\n\n/\n Serialize a Pseudopotential to UPF v1 format.\n \n NOTE: UPF v1 is a legacy format. This serializer produces valid UPF v1\n * but UPF v2 is preferred for new files.\n /\nexport function toUPFv1(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n // Version line\n lines.push(\" 0\");\n lines.push(\"<PP_HEADER>\");\n lines.push(` '${pp.header.element}'`);\n lines.push(` '${pp.header.pseudoType}'`);\n lines.push(` ${pp.header.coreCorrection ? \".true.\" : \".false.\"} nlcc`);\n lines.push(` '${pp.header.functional}' dft`);\n lines.push(` ${pp.header.zValence.toFixed(8)} zp`);\n lines.push(` ${pp.header.totalPsenergy.toFixed(8)} etotps`);\n lines.push(` ${pp.header.wfcCutoff.toFixed(2)} ${pp.header.rhoCutoff.toFixed(2)} ecutwfc,ecutrho`);\n lines.push(` ${pp.header.lMax} 'lmax'`);\n lines.push(` ${pp.mesh.r.length} 'mesh'`);\n lines.push(` ${pp.pswfc.length} ${pp.nonlocal.betas.length} 'nwfc nbeta'`);\n\n // Wavefunction labels\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(4)}`);\n }\n\n lines.push(\"</PP_HEADER>\");\n\n lines.push(\"<PP_MESH>\");\n lines.push(\"<PP_R>\");\n lines.push(formatDataArray(pp.mesh.r));\n lines.push(\"</PP_R>\");\n lines.push(\"<PP_RAB>\");\n lines.push(formatDataArray(pp.mesh.rab));\n lines.push(\"</PP_RAB>\");\n lines.push(\"</PP_MESH>\");\n\n if (pp.nlcc) {\n lines.push(\"<PP_NLCC>\");\n lines.push(formatDataArray(pp.nlcc));\n lines.push(\"</PP_NLCC>\");\n }\n\n lines.push(\"<PP_LOCAL>\");\n lines.push(formatDataArray(pp.local.vloc));\n lines.push(\"</PP_LOCAL>\");\n\n lines.push(\"<PP_NONLOCAL>\");\n for (let i = 0; i < pp.nonlocal.betas.length; i++) {\n const beta = pp.nonlocal.betas[i];\n lines.push(`<PP_BETA>`);\n lines.push(` ${i + 1} ${beta.angularMomentum} '${beta.label}'`);\n lines.push(` ${pp.mesh.r.length}`);\n lines.push(formatDataArray(beta.beta));\n lines.push(`</PP_BETA>`);\n }\n lines.push(\"<PP_DIJ>\");\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n lines.push(` ${nb} ${mb} ${formatFortranNumber(val)}`);\n }\n lines.push(\"</PP_DIJ>\");\n lines.push(\"</PP_NONLOCAL>\");\n\n if (pp.pswfc.length > 0) {\n lines.push(\"<PP_PSWFC>\");\n for (const wfc of pp.pswfc) {\n lines.push(` '${wfc.label ?? \"wfc\"}' ${wfc.l} ${wfc.occupation.toFixed(8)}`);\n lines.push(formatDataArray(wfc.chi));\n }\n lines.push(\"</PP_PSWFC>\");\n }\n\n lines.push(\"<PP_RHOATOM>\");\n lines.push(formatDataArray(pp.rhoatom));\n lines.push(\"</PP_RHOATOM>\");\n\n return lines.join(\"\\n\");\n}\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported energy unit identifiers. /\nexport type EnergyUnits = \"eV\" \| \"Hartree\" \| \"Rydberg\" \| \"kJ/mol\" \| \"kcal/mol\";\n\nconst EnergyConversions: Record<EnergyUnits, number> = {\n eV: 1,\n Hartree: 27.2114,\n Rydberg: 13.6057,\n \"kJ/mol\": 0.0103643,\n \"kcal/mol\": 0.0433641,\n};\n\nconst EnergyAliases: Record<string, EnergyUnits> = {\n Ha: \"Hartree\",\n Ry: \"Rydberg\",\n ev: \"eV\",\n electronvolt: \"eV\",\n};\n\n/* Unit system for energy conversions with eV as base. /\nexport const EnergyUnitSystem = {\n conversions: EnergyConversions,\n aliases: EnergyAliases,\n\n convert(value: number, from: EnergyUnits \| string, to: EnergyUnits \| string) {\n return convertMeasurement(\n value,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: EnergyUnits \| string,\n to: EnergyUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as EnergyUnits,\n to as EnergyUnits,\n EnergyConversions,\n EnergyAliases,\n );\n },\n};\n","import { convertMeasurement, convertMeasurementArray } from \"./converter\";\n\n/* Supported angle unit identifiers. /\nexport type AngleUnits = \"rad\" \| \"deg\" \| \"grad\";\n\nconst AngleConversions: Record<AngleUnits, number> = {\n rad: 1,\n deg: Math.PI / 180,\n grad: Math.PI / 200,\n};\n\nconst AngleAliases: Record<string, AngleUnits> = {\n \"°\": \"deg\",\n deg: \"deg\",\n rad: \"rad\",\n gon: \"grad\",\n};\n\n/* Unit system for angle conversions with radian as base. /\nexport const AngleUnitSystem = {\n conversions: AngleConversions,\n aliases: AngleAliases,\n\n convert(value: number, from: AngleUnits \| string, to: AngleUnits \| string) {\n return convertMeasurement(\n value,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n },\n\n convertArray(\n arr: number[],\n from: AngleUnits \| string,\n to: AngleUnits \| string,\n ) {\n return convertMeasurementArray(\n arr,\n from as AngleUnits,\n to as AngleUnits,\n AngleConversions,\n AngleAliases,\n );\n },\n};\n","/\n Unit conversion helpers for pseudopotentials.\n \n Canonical in-memory units: Rydberg (energy) / Bohr (length) — the\n * UPF-native system. Hartree-based formats (PSP8, FHI/CPI, PSML, GTH) convert\n * on parse and back on serialize. Both factors are exact powers of two, so\n * same-format round-trips stay bit-exact.\n /\n\nimport type { Pseudopotential } from \"./pseudopotential\";\n\nimport { EnergyUnitSystem } from \"../units\";\n\n/\n Hartree → Rydberg factor, derived from the built-in EnergyUnitSystem so\n * there is a single source of truth for conversion factors.\n \n This resolves to exactly 2 (27.2114/13.6057 in floating point), which is\n * what keeps same-format round-trips bit-exact. The factor is resolved ONCE\n * here and hot loops multiply by it directly — never call\n * EnergyUnitSystem.convert per value: it performs alias lookups plus two\n * roundings per call, so (v27.2114)/13.6057 differs from v2 by 1 ulp for\n * some doubles (e.g. -4.8696255250391e-8) and costs a call per element.\n * See the \"pseudo units\" benchmarks for the measured gap.\n /\nexport const HARTREE_TO_RYDBERG: number = EnergyUnitSystem.convert(\n 1,\n \"Hartree\",\n \"Rydberg\",\n);\n\n/* Rydberg → Hartree factor, derived from the built-in EnergyUnitSystem (exactly 0.5). /\nexport const RYDBERG_TO_HARTREE: number = EnergyUnitSystem.convert(\n 1,\n \"Rydberg\",\n \"Hartree\",\n);\n\n/* Alias used in adapters: energies stored in Hartree files → canonical Ry. /\nexport const HA_TO_RY = HARTREE_TO_RYDBERG;\n\n/* Alias used in adapters: canonical Ry → Hartree for file output. /\nexport const RY_TO_HA = RYDBERG_TO_HARTREE;\n\n/* Scale a single energy value (Hartree → Ry). /\nexport function haToRy(value: number): number {\n return value HA_TO_RY;\n}\n\n/** Scale a single energy value (Ry → Hartree). /\nexport function ryToHa(value: number): number {\n return value RY_TO_HA;\n}\n\n/** Scale every entry of an energy array (Hartree → Ry), returning a new array. /\nexport function haArrayToRy(values: Float64Array): Float64Array {\n const out = new Float64Array(values.length);\n for (let i = 0; i < values.length; i++) out[i] = values[i] HA_TO_RY;\n return out;\n}\n\n/** Scale every entry of an energy array (Ry → Hartree), returning a new array. /\nexport function ryArrayToHa(values: Float64Array): Float64Array {\n const out = new Float64Array(values.length);\n for (let i = 0; i < values.length; i++) out[i] = values[i] RY_TO_HA;\n return out;\n}\n\n/*\n Energy-carrying fields converted when crossing the Hartree boundary.\n \n Converted (energies, in Ry canonically):\n * header.totalPsenergy / wfcCutoff / rhoCutoff, local.vloc, semilocal vnl,\n * D_ij values, wfc pseudoEnergy, paw.coreEnergy, paw.aeVloc,\n * gth.cexpPpl / hprj / kprj.\n \n NOT converted (lengths, densities, dimensionless shapes):\n * mesh r/rab/rmax/dx/xmin/zmesh, cutoff radii, rhoatom, nlcc, occupations,\n * chi/aewfc wavefunctions and beta projectors (L²-normalized shapes, plus\n * their Gaussian tails reach denormal magnitudes that no scaling round-trips\n * bit-exactly), gth rLoc/rPs/nElec.\n /\n\n/\n Scale all energy-carrying fields of a Hartree-sourced pseudopotential to\n * canonical Ry. Mutates in place and returns the same object.\n /\nexport function scaleHaToRy(pp: Pseudopotential): Pseudopotential {\n const h = pp.header;\n h.totalPsenergy = haToRy(h.totalPsenergy);\n h.wfcCutoff = haToRy(h.wfcCutoff);\n h.rhoCutoff = haToRy(h.rhoCutoff);\n pp.local.vloc = haArrayToRy(pp.local.vloc);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) sl.vnl = haArrayToRy(sl.vnl);\n }\n for (const entry of pp.nonlocal.dij) entry[2] = haToRy(entry[2]);\n for (const wfc of pp.pswfc) {\n if (wfc.pseudoEnergy != null) wfc.pseudoEnergy = haToRy(wfc.pseudoEnergy);\n }\n if (pp.paw) {\n pp.paw.coreEnergy = haToRy(pp.paw.coreEnergy);\n pp.paw.aeVloc = haArrayToRy(pp.paw.aeVloc);\n }\n if (pp.gth) {\n pp.gth.cexpPpl = pp.gth.cexpPpl.map(haToRy);\n pp.gth.hprj = pp.gth.hprj.map((m) => m.map((row) => row.map(haToRy)));\n if (pp.gth.kprj) {\n pp.gth.kprj = pp.gth.kprj.map((m) => m.map((row) => row.map(haToRy)));\n }\n }\n return pp;\n}\n\n/\n Scale all energy-carrying fields of a canonical (Ry) pseudopotential back\n * to Hartree for Hartree-based file output. Mutates in place.\n /\nexport function scaleRyToHa(pp: Pseudopotential): Pseudopotential {\n const h = pp.header;\n h.totalPsenergy = ryToHa(h.totalPsenergy);\n h.wfcCutoff = ryToHa(h.wfcCutoff);\n h.rhoCutoff = ryToHa(h.rhoCutoff);\n pp.local.vloc = ryArrayToHa(pp.local.vloc);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) sl.vnl = ryArrayToHa(sl.vnl);\n }\n for (const entry of pp.nonlocal.dij) entry[2] = ryToHa(entry[2]);\n for (const wfc of pp.pswfc) {\n if (wfc.pseudoEnergy != null) wfc.pseudoEnergy = ryToHa(wfc.pseudoEnergy);\n }\n if (pp.paw) {\n pp.paw.coreEnergy = ryToHa(pp.paw.coreEnergy);\n pp.paw.aeVloc = ryArrayToHa(pp.paw.aeVloc);\n }\n if (pp.gth) {\n pp.gth.cexpPpl = pp.gth.cexpPpl.map(ryToHa);\n pp.gth.hprj = pp.gth.hprj.map((m) => m.map((row) => row.map(ryToHa)));\n if (pp.gth.kprj) {\n pp.gth.kprj = pp.gth.kprj.map((m) => m.map((row) => row.map(ryToHa)));\n }\n }\n return pp;\n}\n","import { PeriodicTable } from \"../../data/periodictable/atomicData\";\n\n/* Reverse lookup: element symbol → atomic number. /\nconst SymbolToZ = new Map<string, number>();\nfor (const [z, info] of Object.entries(PeriodicTable)) {\n SymbolToZ.set(info.symbol, Number(z));\n}\n\n/* Return the element symbol for a given atomic number (1-based). Returns \"X\" if unknown. /\nexport function guessElement(z: number): string {\n const info = PeriodicTable[Math.round(z)];\n return info?.symbol ?? \"X\";\n}\n\n/* Return the atomic number for a given element symbol. Returns 0 if unknown. /\nexport function elementToZ(element: string): number {\n return SymbolToZ.get(element) ?? 0;\n}\n\n/\n Map an ABINIT numeric XC code (pspxc) to a functional name.\n \n Shared by the PSP8 and FHI adapters. Unknown codes fall back to `xc=<n>`.\n /\nexport function pspxcToFunctional(pspxc: number): string {\n const map: Record<number, string> = {\n 1: \"LDA (PW)\",\n 2: \"LDA (PW92)\",\n 6: \"LDA (Wigner)\",\n 7: \"PW92\",\n 11: \"PBE\",\n 14: \"PBEsol\",\n 23: \"B3LYP\",\n };\n return map[pspxc] ?? `xc=${pspxc}`;\n}\n\n/\n Reverse-map a functional name to an ABINIT numeric XC code.\n \n Used when writing PSP8 for objects from formats that store the functional\n * as a string (e.g. via a UPF hop). Returns undefined when unknown.\n /\nexport function functionalToPspxc(functional: string): number \| undefined {\n const map: Record<string, number> = {\n \"LDA (PW)\": 1,\n \"LDA (PW92)\": 2,\n \"LDA (Wigner)\": 6,\n PW92: 7,\n PBE: 11,\n PBEsol: 14,\n B3LYP: 23,\n };\n return map[functional];\n}\n","/\n FHI98PP (.cpi / .fhi) pseudopotential adapter.\n \n Converts between FHI text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n The FHI format stores norm-conserving pseudopotentials in semilocal form\n * on a logarithmic radial grid. Native units: Hartree (energy), Bohr\n * (length) — energies are converted to Ry on parse (×2) and back on\n * serialize (×0.5).\n \n Grid formula: r(i) = (exp(dx * i) - 1) / Z_eff\n * Stored data: V_l(r) = r * [V_nl(r) + Z_ion/r] (semilocal with Coulomb tail)\n \n Loss notes: raw .cpi carries no element symbol or XC name; those fields\n * stay empty. Only semilocal KB-free data is representable, so objects with\n * projectors/D_ij/US/PAW lose that data here; `canWriteFHI()` reports\n * whether conversion is safe.\n \n References:\n * - Fuchs & Scheffler, Comput. Phys. Commun. 119, 67 (1999)\n * - ABINIT format 6: .fhi = ABINIT header + .cpi content\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement, pspxcToFunctional } from \"./elements\";\n\nexport interface FHIConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as FHI.\n * FHI stores norm-conserving semilocal data only.\n /\nexport function canWriteFHI(pp: Pseudopotential): FHIConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType === \"PAW\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.betas.length > 0 \|\| pp.nonlocal.dij.length > 0) {\n reasons.push(\"KB projectors/D_ij have no FHI representation\");\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no FHI representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no FHI representation\");\n }\n if (pp.paw \|\| pp.fullWfc) {\n reasons.push(\"PAW data has no FHI representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse an FHI98PP pseudopotential file — auto-detects format.\n \n - `.fhi` format (ABINIT format 6): 7 ABINIT header lines + .cpi content\n * - `.cpi` format: starts directly with valence data\n \n Detection: if the first non-empty line starts with a digit → `.cpi`;\n * otherwise → `.fhi`.\n /\nexport function fromFHI(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\");\n const firstNonEmpty = allLines.find((l) => l.trim().length > 0);\n if (!firstNonEmpty) throw new Error(\"FHI file too short to parse\");\n\n // .fhi format (ABINIT format 6) starts with a text description.\n // .cpi format starts with a number (Z_val).\n if (/^\\s\\d/.test(firstNonEmpty)) {\n return parseCpi(text);\n }\n return parseFhiHeader(text);\n}\n\n/*\n Parse a raw .cpi body (without ABINIT header).\n \n Format:\n * Line 1: Z_val n_components\n * Lines 2+: legacy zero-header (variable length, scanned for the mesh line)\n * Then: index r(i) V_0(i) V_1(i) ... V_{lmax}(i) [f_core f_core' f_core'']\n /\nfunction parseCpi(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 4) {\n throw new Error(\"FHI file too short to parse\");\n }\n\n // Line 1: Z_val, n_components\n const line1 = allLines[0].trim().split(/\\s+/);\n const zValence = parseFortranNumber(line1[0]);\n const nComponents = parseIntSafe(line1[1]);\n const lMax = nComponents - 1;\n\n // Lines 2+: legacy header (variable number of zero lines).\n // Scan for the mesh line: first token is a positive integer (mesh_max),\n // second token is a floating-point number (dx).\n let meshLineIdx = 1;\n for (; meshLineIdx < allLines.length; meshLineIdx++) {\n const parts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n if (parts.length >= 2) {\n const firstInt = parseIntSafe(parts[0]);\n if (firstInt > 0) break;\n }\n }\n const meshParts = allLines[meshLineIdx].trim().split(/\\s+/).filter(Boolean);\n const meshMax = parseIntSafe(meshParts[0]);\n const dx = parseFortranNumber(meshParts[1]);\n\n // Parse data block (lines after mesh line)\n // Columns: index, r(i), V_0(i), V_1(i), ... [, f_core, f_core', f_core'']\n const rValues: number[] = [];\n const semilocal: Float64Array[] = [];\n for (let l = 0; l <= lMax; l++) {\n semilocal.push(new Float64Array(meshMax));\n }\n let hasNlcc = false;\n const nlccData: number[] = [];\n\n for (let i = meshLineIdx + 1; i < allLines.length && rValues.length < meshMax; i++) {\n const parts = allLines[i].trim().split(/\\s+/).filter(Boolean);\n if (parts.length < 3) continue;\n\n const idx = parseIntSafe(parts[0]);\n const r = parseFortranNumber(parts[1]);\n\n // Semilocal potentials\n for (let l = 0; l <= lMax && l + 2 < parts.length; l++) {\n semilocal[l][rValues.length] = parseFortranNumber(parts[l + 2]);\n }\n\n // NLCC data (columns after semilocal potentials)\n const nlccStart = nComponents + 2;\n if (parts.length > nlccStart) {\n hasNlcc = true;\n nlccData.push(parseFortranNumber(parts[nlccStart]));\n }\n\n rValues.push(r);\n }\n\n // Build mesh\n const r = new Float64Array(rValues);\n const rmax = r[r.length - 1];\n\n // Compute rab (dr/di) from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n dx,\n rmax,\n r,\n rab,\n };\n\n // Convert semilocal potentials Hartree → Ry. The l=0 channel doubles as\n // the local part (the FHI format has no separate local potential).\n const semilocalRy = semilocal.map(haArrayToRy);\n const local: PseudopotentialLocal = {\n vloc: semilocalRy.length > 0 ? semilocalRy[0] : new Float64Array(r.length),\n };\n\n // Store semilocal potentials\n const semilocalPotentials = semilocalRy.map((vnl, l) => ({\n l,\n vnl,\n }));\n\n // No KB projectors from FHI format — store as semilocal\n const nonlocal: PseudopotentialNonlocal = {\n betas: [],\n dij: [],\n };\n\n // Build rhoatom (approximate from semilocal if available)\n const rhoatom = new Float64Array(r.length);\n\n return {\n format: \"CPI\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"CPI\" },\n header: {\n element: \"\",\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: hasNlcc,\n functional: \"\",\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: 0,\n numberOfProj: 0,\n },\n mesh,\n local,\n semilocal: semilocalPotentials,\n nonlocal,\n pswfc: [],\n rhoatom,\n nlcc: hasNlcc ? new Float64Array(nlccData) : undefined,\n };\n}\n\n/\n Parse an FHI .fhi file (ABINIT format 6).\n * Skips the 7 ABINIT header lines, then parses the .cpi body.\n /\nfunction parseFhiHeader(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\");\n if (allLines.length < 8) {\n throw new Error(\"FHI file too short to parse (.fhi needs 7 header lines)\");\n }\n // Skip 7 ABINIT header lines, then parse as .cpi\n const cpiContent = allLines.slice(7).join(\"\\n\");\n const pp = parseCpi(cpiContent);\n\n pp.provenance = {\n ...pp.provenance,\n notes: \"parsed from .fhi (ABINIT format 6) envelope\",\n };\n\n // Extract metadata from ABINIT header\n const line2 = allLines[1].trim().split(/\\s+/);\n if (line2.length >= 1) {\n const zatom = parseFloat(line2[0]);\n if (zatom > 0) pp.header.element = guessElement(zatom);\n }\n if (line2.length >= 2) {\n pp.header.zValence = parseFloat(line2[1]);\n }\n\n const line3 = allLines[2].trim().split(/\\s+/);\n if (line3.length >= 3) {\n // pspcod should be 6 for FHI\n const pspxc = parseIntSafe(line3[1]);\n pp.header.xcCode = pspxc;\n pp.header.functional = pspxcToFunctional(pspxc);\n }\n if (line3.length >= 6) {\n pp.header.r2well = parseFortranNumber(line3[5]);\n }\n\n const line4 = allLines[3].trim().split(/\\s+/);\n if (line4.length >= 3) {\n pp.header.rchrg = parseFortranNumber(line4[0]);\n pp.header.fchrg = parseFortranNumber(line4[1]);\n pp.header.qchrg = parseFortranNumber(line4[2]);\n }\n\n return pp;\n}\n\n/\n Serialize a first-class Pseudopotential to FHI .cpi format.\n \n Energies are written in Hartree (native .cpi units). The .cpi body carries\n * no element or functional metadata.\n /\nexport function toFHI(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const nComponents = pp.header.lMax + 1;\n const r = pp.mesh.r;\n\n // Line 1: Z_val, n_components\n lines.push(`${formatFortranNumber(pp.header.zValence, 20)} ${nComponents}`);\n\n // Lines 2-10: legacy header (zeros)\n for (let i = 0; i < 9; i++) {\n lines.push(\" 0.0000 0.0000 0.0000 0.0000\");\n }\n\n // Line 11: mesh_max, dx\n const dx = pp.mesh.dx ?? 0.01;\n lines.push(`${r.length.toString().padStart(6)} ${formatFortranNumber(dx, 20)}`);\n\n // Data block\n for (let i = 0; i < r.length; i++) {\n const parts: string[] = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(r[i], 20),\n ];\n\n // Semilocal potentials (Ry → Ha) or local potential for all channels\n if (pp.semilocal && pp.semilocal.length > 0) {\n for (let l = 0; l <= pp.header.lMax; l++) {\n const sl = pp.semilocal.find((s) => s.l === l);\n parts.push(formatFortranNumber((sl ? sl.vnl[i] : 0) RY_TO_HA, 20));\n }\n } else {\n // Use local potential for all channels\n for (let l = 0; l <= pp.header.lMax; l++) {\n parts.push(formatFortranNumber(pp.local.vloc[i] * RY_TO_HA, 20));\n }\n }\n\n // NLCC data (densities are unit-free)\n if (pp.nlcc && i < pp.nlcc.length) {\n parts.push(formatFortranNumber(pp.nlcc[i], 20));\n }\n\n lines.push(parts.join(\" \"));\n }\n\n return lines.join(\"\\n\");\n}\n","/*\n PSP8 (ABINIT format 8) pseudopotential adapter.\n \n PSP8 is a norm-conserving pseudopotential format produced by ONCVPSP\n * and used widely in the ABINIT/PseudoDojo ecosystem. This adapter converts\n * between PSP8 text and the first-class Pseudopotential object (canonical\n * units Ry / Bohr).\n \n Native units: Hartree (energy), Bohr (length). Energies are converted to\n * Ry on parse (×2) and back to Hartree on serialize (×0.5).\n * Grid: Linear, r(i) = (i-1) * dr, starting at r=0.\n \n Loss notes: PSP8 carries only KB projectors (no semilocal, no PAW, no\n * augmentation charge, no pseudo-wavefunctions). US/PAW objects cannot be\n * faithfully written; `canWritePSP8()` reports whether conversion is safe.\n \n Reference: https://docs.abinit.org/developers/psp8_info/\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFortranNumber,\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n parseIntSafe,\n} from \"./fortran-helpers\";\n\nimport { guessElement, elementToZ, pspxcToFunctional, functionalToPspxc } from \"./elements\";\n\nexport interface PSP8ConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as PSP8.\n * PSP8 supports norm-conserving KB data only: no US/PAW, no augmentation,\n * no spin-orbit coupling, no semilocal potentials.\n /\nexport function canWritePSP8(pp: Pseudopotential): PSP8ConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType !== \"NC\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no PSP8 representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no PSP8 representation\");\n }\n if (pp.semilocal && pp.semilocal.length > 0) {\n reasons.push(\"semilocal potentials are not written to PSP8\");\n }\n if (pp.paw \|\| pp.fullWfc) {\n reasons.push(\"PAW data has no PSP8 representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse a PSP8 pseudopotential file into a first-class Pseudopotential.\n \n Structure:\n * Header (6-7 lines):\n * Line 1: title\n * Line 2: zatom, zion, pspd\n * Line 3: pspcod(=8), pspxc, lmax, lloc, mmax, r2well\n * Line 4: rchrg, fchrg, qchrg\n * Line 5: nproj(0..lmax)\n * Line 6: extension_switch\n * Line 7 (if extension_switch=2 or 3): nprojso(1..lmax)\n \n Data blocks:\n * For each l with nproj(l) > 0: projector block\n * Local potential block\n * If extension_switch=2 or 3: SO projector blocks\n * If fchrg > 0: NLCC block\n /\nexport function fromPSP8(text: string): Pseudopotential {\n const allLines = text.split(\"\\n\").filter((l) => l.trim().length > 0);\n if (allLines.length < 6) {\n throw new Error(\"PSP8 file too short to parse\");\n }\n\n let lineIdx = 0;\n\n // Line 1: title\n const title = allLines[lineIdx++].trim();\n\n // Line 2: zatom, zion, pspd\n const line2 = allLines[lineIdx++].trim().split(/\\s+/);\n const zatom = parseFortranNumber(line2[0]);\n const zion = parseFortranNumber(line2[1]);\n const pspd = line2.length > 2 ? line2[2] : \"\";\n\n // Line 3: pspcod, pspxc, lmax, lloc, mmax, r2well\n const line3 = allLines[lineIdx++].trim().split(/\\s+/);\n const pspcod = parseIntSafe(line3[0]);\n if (pspcod !== 8) {\n throw new Error(`Expected pspcod=8 for PSP8 format, got ${pspcod}`);\n }\n const pspxc = parseIntSafe(line3[1]);\n const lmax = parseIntSafe(line3[2]);\n const lloc = parseIntSafe(line3[3]);\n const mmax = parseIntSafe(line3[4]);\n const r2well = line3.length > 5 ? parseFortranNumber(line3[5]) : undefined;\n\n // Line 4: rchrg, fchrg, qchrg\n const line4 = allLines[lineIdx++].trim().split(/\\s+/);\n const rchrg = parseFortranNumber(line4[0]);\n const fchrg = parseFortranNumber(line4[1]);\n const qchrg = line4.length > 2 ? parseFortranNumber(line4[2]) : 0;\n\n // Line 5: nproj(0..lmax)\n const line5 = allLines[lineIdx++].trim().split(/\\s+/);\n const nproj: number[] = [];\n for (let l = 0; l <= lmax; l++) {\n nproj.push(l < line5.length ? parseIntSafe(line5[l]) : 0);\n }\n\n // Line 6: extension_switch\n const extensionSwitch = parseIntSafe(allLines[lineIdx++].trim());\n\n // Line 7 (if SO): nprojso(1..lmax)\n const nprojso: number[] = [];\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n const line7 = allLines[lineIdx++].trim().split(/\\s+/);\n for (let l = 1; l <= lmax; l++) {\n nprojso.push(l - 1 < line7.length ? parseIntSafe(line7[l - 1]) : 0);\n }\n }\n\n const hasSo = extensionSwitch === 2 \|\| extensionSwitch === 3;\n const hasRhoatom = extensionSwitch === 1 \|\| extensionSwitch === 3;\n\n // Read the radial grid from the first data block (all blocks share it).\n // We collect r(i) here as blocks are consumed, then validate at the end.\n const rValues = new Float64Array(mmax);\n\n const readDataBlock = (\n cols: number,\n skipHeader = true,\n ): { headerParts: string[]; grid: Float64Array; data: Float64Array[] } => {\n const headerParts = skipHeader\n ? allLines[lineIdx++].trim().split(/\\s+/)\n : [];\n const grid = new Float64Array(mmax);\n const data: Float64Array[] = [];\n for (let p = 0; p < cols; p++) data.push(new Float64Array(mmax));\n for (let i = 0; i < mmax && lineIdx < allLines.length; i++) {\n const parts = allLines[lineIdx++].trim().split(/\\s+/);\n if (parts.length >= 2) grid[i] = parseFortranNumber(parts[1]);\n for (let p = 0; p < cols && p + 2 < parts.length; p++) {\n data[p][i] = parseFortranNumber(parts[p + 2]);\n }\n }\n return { headerParts, grid, data };\n };\n\n // Parse projector blocks and local potential\n const betas: BetaProjector[] = [];\n let localVloc: Float64Array = new Float64Array(mmax);\n const ekbValues: number[][] = [];\n let gridSet = false;\n\n const adoptGrid = (grid: Float64Array): void => {\n if (!gridSet) {\n rValues.set(grid);\n gridSet = true;\n }\n };\n\n // Data blocks appear in l order. If lloc <= lmax, the local potential\n // replaces the projector block at position lloc.\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) {\n // Local potential block: header line carries just the l value.\n const { headerParts, grid, data } = readDataBlock(1);\n void headerParts;\n adoptGrid(grid);\n localVloc = data[0];\n } else if (nproj[l] > 0) {\n // Projector block: header line is \"l ekb(1) ekb(2) ...\".\n const { headerParts, grid, data } = readDataBlock(nproj[l]);\n adoptGrid(grid);\n const blockL = parseIntSafe(headerParts[0]);\n const ekb: number[] = [];\n for (let p = 1; p < headerParts.length; p++) {\n ekb.push(parseFortranNumber(headerParts[p]));\n }\n ekbValues.push(ekb);\n\n // Create one beta projector per ekb value. Beta arrays are\n // L2-normalized shapes and stay in file units; energies (ekb, vloc)\n // convert separately.\n for (let p = 0; p < nproj[l]; p++) {\n betas.push({\n angularMomentum: Number.isNaN(blockL) ? l : blockL,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}`,\n beta: data[p],\n });\n }\n }\n }\n\n // If lloc > lmax, local potential comes after all projector blocks\n if (lloc > lmax) {\n const { grid, data } = readDataBlock(1);\n adoptGrid(grid);\n localVloc = data[0];\n }\n localVloc = haArrayToRy(localVloc);\n\n // Build D_ij matrix (Ha → Ry) from ekb values.\n // For single projectors per l: dij[i][i] = ekb[i]; block-diagonal otherwise.\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n let ekbIdx = 0;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) continue;\n if (nproj[l] > 0) {\n const nProjL = nproj[l];\n const ekbL = ekbValues[ekbIdx++] ?? [];\n for (let i = 0; i < nProjL; i++) {\n for (let j = 0; j < nProjL; j++) {\n const val = i === j ? haToRy(ekbL[i] ?? 1.0) : 0;\n dij.push([projIdx + i, projIdx + j, val]);\n }\n }\n projIdx += nProjL;\n }\n }\n\n // Parse SO projector blocks (extension_switch == 2 or 3).\n // ekbso values are stored as diagonal D_ij entries for the \"-so\" projectors.\n if (hasSo) {\n for (let l = 1; l <= lmax; l++) {\n const nProjSo = nprojso[l - 1] ?? 0;\n if (nProjSo > 0) {\n const { headerParts, data } = readDataBlock(nProjSo);\n const soEkb: number[] = [];\n for (let p = 1; p < headerParts.length; p++) {\n soEkb.push(parseFortranNumber(headerParts[p]));\n }\n for (let p = 0; p < nProjSo; p++) {\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}-so`,\n beta: data[p],\n });\n dij.push([projIdx + p, projIdx + p, haToRy(soEkb[p] ?? 1.0)]);\n }\n projIdx += nProjSo;\n }\n }\n }\n\n // Parse NLCC block if present (no header line — mmax bare data lines)\n let nlcc: Float64Array \| undefined;\n if (fchrg > 0) {\n const { data } = readDataBlock(1, false);\n nlcc = data[0];\n }\n\n // Parse pseudo valence charge block if extension_switch == 1 or 3\n // (no header line — mmax bare data lines)\n const rhoatom = new Float64Array(mmax);\n if (hasRhoatom) {\n const { data } = readDataBlock(1, false);\n rhoatom.set(data[0]);\n }\n\n // Build mesh (linear grid, Bohr)\n const rmax = rValues[mmax - 1] \|\| 0;\n const dr = mmax > 1 && rmax > 0 ? rValues[1] - rValues[0] : 0;\n const rab = new Float64Array(mmax).fill(dr);\n\n const mesh: PseudopotentialMesh = {\n gridType: \"linear\",\n rmax,\n r: rValues,\n rab,\n };\n\n // Guess element from zatom\n const element = guessElement(zatom);\n\n // Map pspxc to functional string\n const functional = pspxcToFunctional(pspxc);\n\n return {\n format: \"PSP8\",\n units: { ...CANONICAL_UNITS },\n provenance: { sourceFormat: \"PSP8\", creator: title, date: pspd },\n header: {\n element,\n generated: title,\n date: pspd,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: fchrg > 0,\n functional,\n zValence: zion,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: lmax,\n lMaxRho: lmax,\n lLocal: lloc,\n meshSize: mmax,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n xcCode: pspxc,\n extensionSwitch,\n r2well,\n rchrg,\n fchrg,\n qchrg,\n },\n mesh,\n local: { vloc: localVloc } satisfies PseudopotentialLocal,\n nonlocal: { betas, dij } satisfies PseudopotentialNonlocal,\n pswfc: [],\n rhoatom,\n nlcc,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to PSP8 format.\n \n Energies (vloc, projectors, ekb) are written back in Hartree. Only\n * norm-conserving data is supported; use `canWritePSP8()` to check first.\n /\nexport function toPSP8(pp: Pseudopotential): string {\n const lines: string[] = [];\n\n const lmax = pp.header.lMax;\n const mmax = pp.mesh.r.length;\n // QE uses lLocal < 0 for \"no explicit local channel\"; PSP8 has no such\n // notion, so map it to \"separate local block\" (lloc > lmax), which carries\n // the same semantics (local potential tabulated on its own).\n const rawLloc = pp.header.lLocal ?? 0;\n const lloc = rawLloc < 0 ? lmax + 1 : rawLloc;\n\n // Split betas into regular and spin-orbit groups (label suffix \"-so\").\n const isSoBeta = (b: BetaProjector): boolean => b.label.endsWith(\"-so\");\n const regularBetas = pp.nonlocal.betas.filter((b) => !isSoBeta(b));\n const soBetas = pp.nonlocal.betas.filter(isSoBeta);\n\n const nproj: number[] = new Array(lmax + 1).fill(0);\n for (const beta of regularBetas) {\n if (beta.angularMomentum <= lmax && beta.angularMomentum >= 0) {\n nproj[beta.angularMomentum]++;\n }\n }\n const nprojso: number[] = new Array(Math.max(lmax, 0)).fill(0);\n for (const beta of soBetas) {\n if (beta.angularMomentum >= 1 && beta.angularMomentum <= lmax) {\n nprojso[beta.angularMomentum - 1]++;\n }\n }\n\n // extension_switch: prefer the stored value; derive it for objects from\n // formats without the concept (e.g. UPF) from the data actually present.\n const hasRhoatomData = pp.rhoatom.some((v) => v !== 0);\n const extensionSwitch =\n pp.header.extensionSwitch ??\n (hasRhoatomData ? 1 : 0) + (soBetas.length > 0 ? 2 : 0);\n\n // Header\n const zatom = elementToZ(pp.header.element);\n lines.push(pp.header.generated ?? `${pp.header.element} ${pp.header.functional}`);\n const pspd = pp.header.date ?? \"000000\";\n lines.push(\n `${zatom.toFixed(4).padStart(12)} ${pp.header.zValence.toFixed(4).padStart(12)} ${pspd.padStart(8)}`,\n );\n // XC code: prefer the stored value; reverse-map the functional string for\n // objects arriving via formats that only carry the name (e.g. UPF).\n const pspxc =\n pp.header.xcCode ?? functionalToPspxc(pp.header.functional) ?? 0;\n lines.push(\n ` 8 ${pspxc} ${lmax} ${lloc} ${mmax} ${pp.header.r2well ?? 0}`,\n );\n const rchrg = pp.header.rchrg ?? 0;\n const fchrg =\n pp.header.fchrg ?? (pp.nlcc ? 1.0 : pp.header.coreCorrection ? 1.0 : 0.0);\n const qchrg = pp.header.qchrg ?? 0;\n lines.push(`${rchrg.toFixed(4).padStart(12)} ${fchrg.toFixed(4).padStart(12)} ${qchrg.toFixed(4).padStart(12)}`);\n lines.push(` ${nproj.join(\" \")}`);\n lines.push(` ${extensionSwitch}`);\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n lines.push(` ${nprojso.join(\" \")}`);\n }\n\n // Projector blocks (regular). ekb recovered from diagonal D_ij entries.\n const ekb = pp.nonlocal.dij;\n const ekbOf = (globalIdx: number): number => {\n const entry = ekb.find(([nb, mb]) => nb === globalIdx && mb === globalIdx);\n return entry ? entry[2] RY_TO_HA : 1.0;\n };\n\n let projOffset = 1;\n for (let l = 0; l <= lmax; l++) {\n if (l === lloc && lloc <= lmax) {\n // Local potential replaces the block at the lloc position.\n lines.push(` ${l}`);\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.local.vloc[i] * RY_TO_HA)}`,\n );\n }\n continue;\n }\n const lBetas = regularBetas.filter((b) => b.angularMomentum === l);\n if (lBetas.length === 0) continue;\n\n const ekbValues = lBetas.map((_, i) => ekbOf(projOffset + i));\n lines.push(` ${l} ${ekbValues.map((e) => formatFortranNumber(e)).join(\" \")}`);\n\n for (let i = 0; i < mmax; i++) {\n const parts = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(pp.mesh.r[i]),\n ];\n for (const beta of lBetas) {\n parts.push(formatFortranNumber(beta.beta[i] ?? 0));\n }\n lines.push(parts.join(\" \"));\n }\n\n projOffset += lBetas.length;\n }\n\n // Local potential block (Hartree) — only when it does not replace a\n // channel block above (lloc > lmax means a separate trailing block).\n if (lloc > lmax) {\n lines.push(` ${lloc}`);\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.local.vloc[i] * RY_TO_HA)}`,\n );\n }\n }\n\n // SO projector blocks\n if (extensionSwitch === 2 \|\| extensionSwitch === 3) {\n for (let l = 1; l <= lmax; l++) {\n const lBetas = soBetas.filter((b) => b.angularMomentum === l);\n if (lBetas.length === 0) continue;\n const ekbValues = lBetas.map((_, i) => ekbOf(projOffset + i));\n lines.push(` ${l} ${ekbValues.map((e) => formatFortranNumber(e)).join(\" \")}`);\n for (let i = 0; i < mmax; i++) {\n const parts = [\n (i + 1).toString().padStart(5),\n formatFortranNumber(pp.mesh.r[i]),\n ];\n for (const beta of lBetas) {\n parts.push(formatFortranNumber(beta.beta[i] ?? 0));\n }\n lines.push(parts.join(\" \"));\n }\n projOffset += lBetas.length;\n }\n }\n\n // NLCC block\n if (pp.nlcc) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.nlcc[i])}`,\n );\n }\n }\n\n // Pseudo valence charge block (if extension_switch == 1 or 3)\n if (extensionSwitch === 1 \|\| extensionSwitch === 3) {\n for (let i = 0; i < mmax; i++) {\n lines.push(\n `${(i + 1).toString().padStart(5)} ${formatFortranNumber(pp.mesh.r[i])} ${formatFortranNumber(pp.rhoatom[i])}`,\n );\n }\n }\n\n return lines.join(\"\\n\");\n}\n","/*\n PSML (PSeudopotential Markup Language) pseudopotential adapter.\n \n Converts between PSML text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n PSML is an XML-based format for norm-conserving pseudopotentials,\n * created by the ESL (Electronic Structure Library) initiative.\n * Native units: Hartree (energy), Bohr (length) — mandatory per schema.\n * Energies are converted to Ry on parse (×2) and back on serialize (×0.5).\n \n Loss notes: PSML stores only the diagonal KB energies (ekb); off-diagonal\n * D_ij couplings have no representation. PAW/US/augmentation/spin-orbit\n * data cannot round-trip; use `canWritePSML()` to check first.\n \n Reference: https://siesta-project.github.io/psml-docs/\n * Schema: http://esl.cecam.org/PSML/ns/1.2\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialNonlocal,\n BetaProjector,\n PseudopotentialWfc,\n Provenance,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n haArrayToRy,\n} from \"../../pseudopotential/units\";\n\nimport {\n parseFloat64Array,\n formatFortranNumber,\n formatDataArray,\n} from \"./fortran-helpers\";\n\nimport {\n type XmlNode,\n attr,\n attrNum,\n attrInt,\n textOf,\n toArray,\n parseXml,\n} from \"./xml-helpers\";\n\nimport { guessElement, elementToZ } from \"./elements\";\n\nexport interface PSMLConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as PSML.\n * PSML supports norm-conserving data only.\n /\nexport function canWritePSML(pp: Pseudopotential): PSMLConversionCheck {\n const reasons: string[] = [];\n if (pp.header.isUltrasoft \|\| pp.header.isPaw \|\| pp.header.pseudoType !== \"NC\") {\n reasons.push(`pseudoType ${pp.header.pseudoType} is not norm-conserving`);\n }\n if (pp.nonlocal.augmentation) {\n reasons.push(\"augmentation data has no PSML representation\");\n }\n if (pp.header.hasSo \|\| pp.spinOrbit) {\n reasons.push(\"spin-orbit data has no PSML representation\");\n }\n if (pp.paw \|\| pp.fullWfc \|\| pp.gipaw) {\n reasons.push(\"PAW/GIPAW data has no PSML representation\");\n }\n return { ok: reasons.length === 0, reasons };\n}\n\n/\n Parse a PSML pseudopotential file into a first-class Pseudopotential.\n /\nexport function fromPSML(text: string): Pseudopotential {\n const parsed = parseXml(text);\n\n // Find root element (may have namespace prefix)\n const root = parsed[\"psml\"] ?? parsed[`${\"http://esl.cecam.org/PSML/ns/1.2\"}:psml`] ?? parsed;\n\n // Provenance\n const provenanceData = root[\"provenance\"];\n let creator: string \| undefined;\n let date: string \| undefined;\n if (provenanceData) {\n const provArr = toArray(provenanceData);\n if (provArr.length > 0) {\n const first = provArr[0];\n creator = attr(first, \"creator\") \|\| undefined;\n date = attr(first, \"date\") \|\| undefined;\n }\n }\n const provenance: Provenance = { sourceFormat: \"PSML\", creator, date };\n\n // Pseudo-atom spec\n const spec = root[\"pseudo-atom-spec\"] ?? {};\n const element = attr(spec, \"atomic-label\") \|\| guessElement(attrInt(spec, \"atomic-number\"));\n const zValence = attrNum(spec, \"z-pseudo\");\n const relativity = attr(spec, \"relativity\") \|\| \"scalar\";\n const coreCorrections = attr(spec, \"core-corrections\") === \"yes\";\n\n // XC functional from libxc-info\n const xcInfo = spec[\"exchange-correlation\"]?.[\"libxc-info\"];\n let functional = \"\";\n if (xcInfo) {\n const funchs = toArray(xcInfo[\"functional\"]);\n functional = funchs.map((f: XmlNode) => attr(f, \"name\")).join(\"+\");\n }\n\n // Grid\n const gridNode = root[\"grid\"];\n let r: Float64Array = new Float64Array(0);\n if (gridNode) {\n const gridData = gridNode[\"grid-data\"];\n if (gridData) r = parseFloat64Array(textOf(gridData));\n }\n if (r.length === 0) throw new Error(\"Missing or empty grid in PSML file\");\n\n // Compute rab from grid\n const rab = new Float64Array(r.length);\n for (let i = 1; i < r.length; i++) {\n rab[i] = r[i] - r[i - 1];\n }\n if (r.length > 1) rab[0] = rab[1];\n\n const mesh: PseudopotentialMesh = {\n gridType: \"custom\",\n rmax: r[r.length - 1],\n r,\n rab,\n };\n\n // Local potential (Hartree → Ry)\n const localNode = root[\"local-potential\"];\n let localVloc: Float64Array = new Float64Array(r.length);\n if (localNode) {\n const dataNode = localNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) localVloc = haArrayToRy(parseFloat64Array(textOf(dataNode)));\n }\n\n // Semilocal potentials (Hartree → Ry)\n const slNode = root[\"semilocal-potentials\"];\n const semilocalPotentials: Pseudopotential[\"semilocal\"] = [];\n const slSet = toArray(slNode);\n if (slSet.length > 0) {\n const slpsNodes = toArray(slSet[0][\"slps\"]);\n for (const slps of slpsNodes) {\n const l = lFromLetter(attr(slps, \"l\"));\n const dataNode = slps[\"radfunc\"]?.[\"data\"];\n const vnl = dataNode\n ? haArrayToRy(parseFloat64Array(textOf(dataNode)))\n : new Float64Array(r.length);\n semilocalPotentials.push({ l, vnl });\n }\n }\n\n // Nonlocal projectors (dimensionless shapes — no conversion)\n const nlNode = root[\"nonlocal-projectors\"];\n const betas: BetaProjector[] = [];\n const nlSet = toArray(nlNode);\n const ekbByIdx = new Map<number, number>();\n if (nlSet.length > 0) {\n const projNodes = toArray(nlSet[0][\"proj\"]);\n let idx = 1;\n for (const proj of projNodes) {\n const l = lFromLetter(attr(proj, \"l\"));\n const ekb = attrNum(proj, \"ekb\");\n ekbByIdx.set(idx, ekb);\n const dataNode = proj[\"radfunc\"]?.[\"data\"];\n const betaData = dataNode\n ? parseFloat64Array(textOf(dataNode))\n : new Float64Array(r.length);\n betas.push({\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${lToLetter(l)}`,\n beta: betaData,\n });\n idx++;\n }\n }\n\n // Build D_ij from ekb values (diagonal; PSML stores no off-diagonal data)\n const dij: Array<[number, number, number]> = [];\n for (const [idx, ekb] of ekbByIdx) {\n dij.push([idx, idx, haToRy(ekb)]);\n }\n\n // Pseudo wavefunctions (dimensionless radial functions — no conversion)\n const pswfcNodes = toArray(root[\"pseudo-wave-functions\"]);\n const pswfc: PseudopotentialWfc[] = [];\n if (pswfcNodes.length > 0) {\n const pswfNodes = toArray(pswfcNodes[0][\"pswf\"]);\n for (const pswf of pswfNodes) {\n const l = lFromLetter(attr(pswf, \"l\"));\n const n = attrInt(pswf, \"n\");\n const dataNode = pswf[\"radfunc\"]?.[\"data\"];\n const chi = dataNode ? parseFloat64Array(textOf(dataNode)) : new Float64Array(r.length);\n pswfc.push({\n l,\n occupation: 0,\n label: `${n}${lToLetter(l)}`,\n n,\n chi,\n });\n }\n }\n\n // Valence charge (density — no conversion; store as rhoatom)\n const vcNode = root[\"valence-charge\"];\n let rhoatom: Float64Array = new Float64Array(r.length);\n if (vcNode) {\n const dataNode = vcNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) rhoatom = parseFloat64Array(textOf(dataNode));\n }\n\n // Core charge (NLCC, density — no conversion)\n const ccNode = root[\"pseudocore-charge\"];\n let nlcc: Float64Array \| undefined;\n if (ccNode) {\n const dataNode = ccNode[\"radfunc\"]?.[\"data\"];\n if (dataNode) nlcc = parseFloat64Array(textOf(dataNode));\n }\n\n return {\n format: \"PSML\",\n units: { ...CANONICAL_UNITS },\n provenance,\n header: {\n element,\n pseudoType: \"NC\",\n relativistic: relativity as PseudopotentialHeader[\"relativistic\"],\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: false,\n hasWfc: pswfc.length > 0,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: coreCorrections,\n functional,\n zValence,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax: semilocalPotentials.length > 0\n ? Math.max(...semilocalPotentials.map((s) => s.l))\n : betas.length > 0\n ? Math.max(...betas.map((b) => b.angularMomentum))\n : 0,\n lMaxRho: 0,\n lLocal: 0,\n meshSize: r.length,\n numberOfWfc: pswfc.length,\n numberOfProj: betas.length,\n },\n mesh,\n local: { vloc: localVloc },\n semilocal: semilocalPotentials.length > 0 ? semilocalPotentials : undefined,\n nonlocal: { betas, dij },\n pswfc,\n rhoatom,\n nlcc,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to PSML format.\n * Energies are written in Hartree (mandatory per the PSML schema).\n /\nexport function toPSML(pp: Pseudopotential): string {\n const r = pp.mesh.r;\n const npts = r.length;\n\n let xml = `<?xml version=\"1.0\" encoding=\"UTF-8\" ?>\\n`;\n xml += `<psml version=\"1.2\" energy_unit=\"hartree\" length_unit=\"bohr\" uuid=\"matsci-parse\">\\n`;\n\n // Provenance: provenance fields take precedence; fall back to the UPF\n // header equivalents so generator stamps survive a hub conversion.\n {\n const provCreator =\n pp.provenance.creator ?? pp.header.generated ?? pp.header.author ?? \"matsci-parse\";\n const provDate =\n pp.provenance.date ?? pp.header.date ?? new Date().toISOString().split(\"T\")[0];\n xml += ` <provenance creator=\"${provCreator}\" date=\"${provDate}\">\\n`;\n xml += ` <annotation type=\"generated-by\" value=\"matsci-parse pseudopotential library\" />\\n`;\n xml += ` </provenance>\\n`;\n }\n\n // Pseudo-atom spec\n xml += ` <pseudo-atom-spec atomic-label=\"${pp.header.element}\" atomic-number=\"${elementToZ(pp.header.element)}\" z-pseudo=\"${pp.header.zValence}\" relativity=\"${pp.header.relativistic}\" core-corrections=\"${pp.header.coreCorrection ? \"yes\" : \"no\"}\">\\n`;\n if (pp.header.functional) {\n xml += ` <exchange-correlation>\\n`;\n xml += ` <libxc-info number-of-functionals=\"0\">\\n`;\n xml += ` <functional name=\"${pp.header.functional}\" />\\n`;\n xml += ` </libxc-info>\\n`;\n xml += ` </exchange-correlation>\\n`;\n }\n xml += ` </pseudo-atom-spec>\\n`;\n\n // Grid\n xml += ` <grid npts=\"${npts}\">\\n`;\n xml += ` <grid-data>\\n`;\n xml += ` ${Array.from(r).map((v) => formatFortranNumber(v).trim()).join(\" \")}\\n`;\n xml += ` </grid-data>\\n`;\n xml += ` </grid>\\n`;\n\n const ha = (v: number): string => formatFortranNumber(v RY_TO_HA).trim();\n const raw = (v: number): string => formatFortranNumber(v).trim();\n\n // Local potential (Ry → Ha)\n xml += ` <local-potential>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">\\n`;\n xml += ` ${Array.from(pp.local.vloc).map(ha).join(\" \")}\\n`;\n xml += ` </data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </local-potential>\\n`;\n\n // Semilocal potentials (Ry → Ha)\n if (pp.semilocal && pp.semilocal.length > 0) {\n xml += ` <semilocal-potentials set=\"scalar_relativistic\">\\n`;\n for (const sl of pp.semilocal) {\n xml += ` <slps l=\"${lToLetter(sl.l)}\" n=\"${sl.l + 1}\" rc=\"0\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${Array.from(sl.vnl).map(ha).join(\" \")}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </slps>\\n`;\n }\n xml += ` </semilocal-potentials>\\n`;\n }\n\n // Nonlocal projectors (shapes unconverted; ekb from diagonal D_ij).\n const nonlocal: PseudopotentialNonlocal = pp.nonlocal;\n if (nonlocal.betas.length > 0) {\n xml += ` <nonlocal-projectors set=\"scalar_relativistic\">\\n`;\n let idx = 1;\n for (const beta of nonlocal.betas) {\n const ekbEntry = nonlocal.dij.find(([nb, mb]) => nb === idx && mb === idx);\n const ekb = ekbEntry ? ekbEntry[2] * RY_TO_HA : 1.0;\n xml += ` <proj l=\"${lToLetter(beta.angularMomentum)}\" seq=\"${idx}\" ekb=\"${formatFortranNumber(ekb).trim()}\" type=\"kb\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${Array.from(beta.beta).map(raw).join(\" \")}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </proj>\\n`;\n idx++;\n }\n xml += ` </nonlocal-projectors>\\n`;\n }\n\n // Pseudo wavefunctions (dimensionless — no conversion)\n if (pp.pswfc.length > 0) {\n xml += ` <pseudo-wave-functions set=\"pseudo\">\\n`;\n for (const wfc of pp.pswfc) {\n xml += ` <pswf l=\"${lToLetter(wfc.l)}\" n=\"${wfc.n ?? wfc.l + 1}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(wfc.chi)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pswf>\\n`;\n }\n xml += ` </pseudo-wave-functions>\\n`;\n }\n\n // Valence charge\n if (pp.rhoatom.length > 0) {\n xml += ` <valence-charge total-charge=\"${pp.header.zValence}\">\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${npts}\">${formatDataArray(pp.rhoatom)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </valence-charge>\\n`;\n }\n\n // Core charge (NLCC)\n if (pp.nlcc && pp.nlcc.length > 0) {\n xml += ` <pseudocore-charge>\\n`;\n xml += ` <radfunc>\\n`;\n xml += ` <data npts=\"${pp.nlcc.length}\">${formatDataArray(pp.nlcc)}</data>\\n`;\n xml += ` </radfunc>\\n`;\n xml += ` </pseudocore-charge>\\n`;\n }\n\n xml += `</psml>\\n`;\n return xml;\n}\n\nfunction lFromLetter(letter: string): number {\n const map: Record<string, number> = { s: 0, p: 1, d: 2, f: 3, g: 4 };\n return map[letter.toLowerCase()] ?? 0;\n}\n\nfunction lToLetter(l: number): string {\n return \"spdfg\"[l] ?? String(l);\n}\n","import type {\n BetaProjector,\n Pseudopotential,\n PseudopotentialWfc,\n} from \"../pseudopotential\";\n\n/** One angular-momentum channel of a pseudopotential. /\nexport interface LChannel {\n /* Angular momentum. /\n l: number;\n /* KB projectors in this channel. /\n betas: BetaProjector[];\n /* Semilocal potential value for this channel, if present. /\n semilocalVnl?: Float64Array;\n /* Pseudo-wavefunctions in this channel. /\n wfcs: PseudopotentialWfc[];\n /* True when this channel is the local channel. /\n isLocal: boolean;\n}\n\n/\n Group projectors, semilocal potentials and wavefunctions by l.\n \n @param pp - The pseudopotential to inspect.\n * @returns Channels sorted by angular momentum.\n /\nexport function listChannels(pp: Pseudopotential): LChannel[] {\n const byL = new Map<number, LChannel>();\n const get = (l: number): LChannel => {\n let ch = byL.get(l);\n if (!ch) {\n ch = {\n l,\n betas: [],\n wfcs: [],\n isLocal: l === pp.header.lLocal,\n };\n byL.set(l, ch);\n }\n return ch;\n };\n for (const beta of pp.nonlocal.betas) get(beta.angularMomentum).betas.push(beta);\n if (pp.semilocal) {\n for (const sl of pp.semilocal) get(sl.l).semilocalVnl = sl.vnl;\n }\n for (const wfc of pp.pswfc) get(wfc.l).wfcs.push(wfc);\n // Surface the local channel when it carries an l label (lLocal < 0 means\n // \"no explicit local channel\", as in some NC files).\n if (pp.header.lLocal >= 0) get(pp.header.lLocal);\n return [...byL.values()].sort((a, b) => a.l - b.l);\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/* Cutoff radii per projector (Bohr), plus header-suggested plane-wave cutoffs (Ry). /\nexport interface CutoffInfo {\n /* Per-projector cutoff radius (cutoffRadius ?? ultrasoftCutoffRadius). /\n projectorCutoffs: Array<{ l: number; label: string; cutoff: number }>;\n /* Suggested wavefunction cutoff from the header (Ry). /\n wfcCutoff: number;\n /* Suggested charge-density cutoff from the header (Ry). /\n rhoCutoff: number;\n}\n\n/\n Collect cutoff radii and suggested plane-wave cutoffs.\n \n @param pp - The pseudopotential to inspect.\n /\nexport function getCutoffs(pp: Pseudopotential): CutoffInfo {\n return {\n projectorCutoffs: pp.nonlocal.betas.map((beta) => ({\n l: beta.angularMomentum,\n label: beta.label,\n cutoff: beta.cutoffRadius ?? beta.ultrasoftCutoffRadius,\n })),\n wfcCutoff: pp.header.wfcCutoff,\n rhoCutoff: pp.header.rhoCutoff,\n };\n}\n","/* Options for radial grid generation. /\nexport interface RadialGridOptions {\n /* Number of grid points. /\n npts: number;\n /* Maximum radius in Bohr. /\n rmax: number;\n /* \"log\" mimics the GTH/log grids; \"linear\" mimics PSP8. /\n type?: \"log\" \| \"linear\";\n}\n\n/\n Generate a radial grid with trapezoidal-style integration weights.\n \n @param options - Grid size, extent and type.\n /\nexport function makeRadialGrid(options: RadialGridOptions): {\n r: Float64Array;\n rab: Float64Array;\n} {\n const { npts, rmax, type = \"log\" } = options;\n if (!Number.isInteger(npts) \|\| npts < 1) {\n throw new Error(`makeRadialGrid requires npts >= 1, got ${npts}`);\n }\n // A single-point grid is just the endpoint with zero weight.\n if (npts === 1) {\n return { r: new Float64Array([rmax]), rab: new Float64Array([0]) };\n }\n const r = new Float64Array(npts);\n const rab = new Float64Array(npts);\n if (type === \"linear\") {\n const dr = npts > 1 ? rmax / (npts - 1) : 0;\n for (let i = 0; i < npts; i++) {\n r[i] = i dr;\n rab[i] = dr;\n }\n } else {\n const dx = Math.log(rmax) / (npts - 1);\n for (let i = 0; i < npts; i++) {\n r[i] = Math.exp(dx * i);\n rab[i] = r[i] * dx;\n }\n if (npts > 1) {\n r[0] = r[1] * 0.01;\n rab[0] = r[0] * dx;\n }\n }\n return { r, rab };\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/** Piecewise-linear interpolation of y(x) at a single point. /\nfunction interp1(x: Float64Array, y: Float64Array, xi: number): number {\n if (xi <= x[0]) return y[0];\n if (xi >= x[x.length - 1]) return y[y.length - 1];\n let lo = 0;\n let hi = x.length - 1;\n while (hi - lo > 1) {\n const mid = (lo + hi) >> 1;\n if (x[mid] <= xi) lo = mid;\n else hi = mid;\n }\n const t = (xi - x[lo]) / (x[hi] - x[lo]);\n return y[lo] + t (y[hi] - y[lo]);\n}\n\n/** Resample every radial array of a pseudopotential onto a new grid. /\nfunction resampleArray(\n x: Float64Array,\n y: Float64Array,\n newX: Float64Array,\n): Float64Array {\n const out = new Float64Array(newX.length);\n for (let i = 0; i < newX.length; i++) out[i] = interp1(x, y, newX[i]);\n return out;\n}\n\n/\n Resample a pseudopotential onto a new radial grid (the grid converter).\n * Returns a new object; the header mesh counters and provenance notes are\n * updated accordingly.\n \n @param pp - The pseudopotential to resample.\n * @param newR - The new radial grid in Bohr.\n /\nexport function resampleLinear(\n pp: Pseudopotential,\n newR: Float64Array,\n): Pseudopotential {\n const oldR = pp.mesh.r;\n const rab = new Float64Array(newR.length);\n for (let i = 1; i < newR.length; i++) rab[i] = newR[i] - newR[i - 1];\n if (newR.length > 1) rab[0] = rab[1];\n\n const betas = pp.nonlocal.betas.map((beta) => ({\n ...beta,\n beta: resampleArray(oldR, beta.beta, newR),\n }));\n const semilocal = pp.semilocal?.map((sl) => ({\n ...sl,\n vnl: resampleArray(oldR, sl.vnl, newR),\n }));\n const pswfc = pp.pswfc.map((wfc) => ({\n ...wfc,\n chi: resampleArray(oldR, wfc.chi, newR),\n }));\n const fullWfc = pp.fullWfc?.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n }));\n const augmentation = pp.nonlocal.augmentation\n ? {\n ...pp.nonlocal.augmentation,\n q: pp.nonlocal.augmentation.q\n ? resampleArray(oldR, pp.nonlocal.augmentation.q, newR)\n : undefined,\n multipoles: pp.nonlocal.augmentation.multipoles\n ? resampleArray(oldR, pp.nonlocal.augmentation.multipoles, newR)\n : undefined,\n qfcoeff: pp.nonlocal.augmentation.qfcoeff\n ? resampleArray(oldR, pp.nonlocal.augmentation.qfcoeff, newR)\n : undefined,\n rinner: pp.nonlocal.augmentation.rinner\n ? resampleArray(oldR, pp.nonlocal.augmentation.rinner, newR)\n : undefined,\n qijl: pp.nonlocal.augmentation.qijl?.map((q) => ({\n ...q,\n qijl: resampleArray(oldR, q.qijl, newR),\n })),\n }\n : undefined;\n\n const resampleIfPresent = (\n arr: Float64Array \| undefined,\n ): Float64Array \| undefined =>\n arr && arr.length > 0 ? resampleArray(oldR, arr, newR) : arr;\n\n const paw = pp.paw\n ? {\n ...pp.paw,\n aeNlcc: resampleIfPresent(pp.paw.aeNlcc) ?? pp.paw.aeNlcc,\n aeVloc: resampleIfPresent(pp.paw.aeVloc) ?? pp.paw.aeVloc,\n aeWfcs: pp.paw.aeWfcs.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n })),\n psWfcs: pp.paw.psWfcs.map((wfc) => ({\n ...wfc,\n aewfc: resampleArray(oldR, wfc.aewfc, newR),\n })),\n }\n : undefined;\n\n const gipaw = pp.gipaw\n ? {\n ...pp.gipaw,\n coreOrbitals: pp.gipaw.coreOrbitals.map((co) => ({\n ...co,\n orbital: resampleArray(oldR, co.orbital, newR),\n })),\n orbitals: pp.gipaw.orbitals.map((orb) => ({\n ...orb,\n aeOrbital: resampleArray(oldR, orb.aeOrbital, newR),\n psOrbital: resampleArray(oldR, orb.psOrbital, newR),\n })),\n vlocAe: resampleIfPresent(pp.gipaw.vlocAe) ?? pp.gipaw.vlocAe,\n vlocPs: resampleIfPresent(pp.gipaw.vlocPs) ?? pp.gipaw.vlocPs,\n }\n : undefined;\n\n const spinOrbit = pp.spinOrbit\n ? {\n relWfcs: pp.spinOrbit.relWfcs.map((wfc) => ({\n ...wfc,\n chi: wfc.chi ? resampleArray(oldR, wfc.chi, newR) : undefined,\n })),\n relBetas: pp.spinOrbit.relBetas.map((beta) => ({\n ...beta,\n beta: beta.beta ? resampleArray(oldR, beta.beta, newR) : undefined,\n })),\n }\n : undefined;\n\n return {\n ...pp,\n header: {\n ...pp.header,\n meshSize: newR.length,\n },\n mesh: {\n ...pp.mesh,\n gridType: \"custom\",\n rmax: newR[newR.length - 1],\n r: newR,\n rab,\n },\n nlcc: pp.nlcc ? resampleArray(oldR, pp.nlcc, newR) : undefined,\n local: { vloc: resampleArray(oldR, pp.local.vloc, newR) },\n semilocal,\n nonlocal: { ...pp.nonlocal, betas, augmentation },\n pswfc,\n fullWfc,\n rhoatom: resampleArray(oldR, pp.rhoatom, newR),\n paw,\n gipaw,\n spinOrbit,\n provenance: {\n ...pp.provenance,\n notes: [\n pp.provenance.notes,\n `resampled from ${oldR.length} to ${newR.length} points`,\n ]\n .filter(Boolean)\n .join(\"; \"),\n },\n };\n}\n","import type {\n BetaProjector,\n Pseudopotential,\n} from \"../pseudopotential\";\n\nimport { listChannels } from \"./listChannels\";\n\n/\n Approximate semilocal potentials from Kleinman-Bylander projectors:\n * V_l(r) = V_loc(r) + Σ_ij β_i(r) D_ij β_j(r) / r².\n \n Note: this assumes the UPF convention of storing β(r)·r. Intended for\n * diagnostics and format bridging, not for production KB generation.\n \n @param pp - The pseudopotential with KB projectors.\n * @returns A new object with derived semilocal potentials attached.\n /\nexport function kbToSemilocal(pp: Pseudopotential): Pseudopotential {\n const r = pp.mesh.r;\n const semilocal = listChannels(pp)\n .filter((ch) => ch.betas.length > 0)\n .map((ch) => {\n const vnl = new Float64Array(r.length);\n const globalIdx = new Map<BetaProjector, number>();\n pp.nonlocal.betas.forEach((b, i) => globalIdx.set(b, i + 1));\n const dOf = (i: number, j: number): number => {\n const entry = pp.nonlocal.dij.find(\n ([nb, mb]) => nb === i && mb === j,\n );\n return entry ? entry[2] : 0;\n };\n for (let k = 0; k < r.length; k++) {\n let v = pp.local.vloc[k];\n const rk = r[k] < 1e-15 ? 1e-15 : r[k];\n for (const bi of ch.betas) {\n for (const bj of ch.betas) {\n const i = globalIdx.get(bi) ?? 0;\n const j = globalIdx.get(bj) ?? 0;\n v += (bi.beta[k] dOf(i, j) * bj.beta[k]) / (rk * rk);\n }\n }\n vnl[k] = v;\n }\n return { l: ch.l, vnl };\n });\n\n return { ...pp, semilocal };\n}\n","import type { Pseudopotential } from \"../pseudopotential\";\n\n/*\n Approximate single-projector KB form from semilocal potentials:\n * β_l(r) = (V_l(r) − V_loc(r))·r / √\|D_l\|, D_l = ∫(V_l − V_loc) r² dr.\n \n Channels with more than one semilocal entry or a vanishing norm are\n * skipped. Intended for diagnostics and format bridging.\n \n @param pp - The pseudopotential with semilocal potentials.\n * @returns A new object with derived KB projectors appended.\n /\nexport function semilocalToKb(pp: Pseudopotential): Pseudopotential {\n const r = pp.mesh.r;\n const rab = pp.mesh.rab;\n const betas = [...pp.nonlocal.betas];\n const dij: Array<[number, number, number]> = [...pp.nonlocal.dij];\n let idx = betas.length + 1;\n\n if (pp.semilocal) {\n for (const sl of pp.semilocal) {\n const dv = new Float64Array(r.length);\n for (let k = 0; k < r.length; k++) dv[k] = sl.vnl[k] - pp.local.vloc[k];\n let d = 0;\n for (let k = 0; k < r.length; k++) d += dv[k] r[k] * r[k] * rab[k];\n if (!Number.isFinite(d) \|\| Math.abs(d) < 1e-12) continue;\n const norm = Math.sqrt(Math.abs(d));\n const sign = d >= 0 ? 1 : -1;\n const beta = new Float64Array(r.length);\n for (let k = 0; k < r.length; k++) beta[k] = (dv[k] * r[k]) / norm;\n betas.push({\n index: idx,\n angularMomentum: sl.l,\n ultrasoftCutoffRadius: r[r.length - 1],\n label: `${sl.l}${\"spdf\"[sl.l] ?? sl.l}`,\n beta,\n });\n dij.push([idx, idx, sign * Math.abs(d)]);\n idx++;\n }\n }\n\n return {\n ...pp,\n header: { ...pp.header, numberOfProj: betas.length },\n nonlocal: { ...pp.nonlocal, betas, dij },\n };\n}\n","/*\n GTH/HGH (Goedecker-Teter-Hutter / Hartwigsen-Goedecker-Hutter) adapter.\n \n Converts between GTH text and the first-class Pseudopotential object\n * (canonical units Ry / Bohr).\n \n GTH/HGH pseudopotentials are analytical, defined by Gaussian functions\n * rather than tabulated on a radial grid. The IR keeps BOTH: the analytical\n * parameters in `gth` (with `provenance.analytical = true`) and an evaluated\n * tabulation on a logarithmic grid for grid-based consumers.\n \n Native units: Hartree (energy), Bohr (length) — analytical parameters are\n * converted to Ry on parse (×2) and back on serialize (×0.5). Length-like\n * parameters (rLoc, rPs) are unit-free here (Bohr in both systems).\n \n Loss notes: k-matrix (SOC) is parsed when present (inline channel-line\n * remainder, or trailing block after the last channel) and round-trips;\n * entries without analytical GTH parameters cannot be written (`toGTH`\n * throws — use `canWriteGTH()` to check first).\n \n Reference:\n * - GTH: Goedecker, Teter, Hutter, PRB 54, 1703 (1996)\n * - HGH: Hartwigsen, Goedecker, Teter, Hutter, PRB 58, 3641 (1998)\n /\n\nimport type {\n Pseudopotential,\n PseudopotentialHeader,\n PseudopotentialMesh,\n PseudopotentialLocal,\n PseudopotentialNonlocal,\n BetaProjector,\n GthData,\n PseudopotentialFormat,\n} from \"../../pseudopotential/pseudopotential\";\n\nimport { CANONICAL_UNITS } from \"../../pseudopotential/pseudopotential\";\nimport {\n RY_TO_HA,\n haToRy,\n} from \"../../pseudopotential/units\";\n\nimport { makeRadialGrid } from \"../../pseudopotential/operations\";\n\nimport {\n parseFortranNumber,\n formatFortranNumber,\n} from \"./fortran-helpers\";\n\nexport interface GTHConversionCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be written as GTH.\n * Tabulated-only data cannot be inverted to analytical GTH form.\n /\nexport function canWriteGTH(pp: Pseudopotential): GTHConversionCheck {\n const reasons: string[] = [];\n if (!pp.gth) {\n reasons.push(\n \"no GTH analytical parameters (tabulated-only data cannot be inverted to GTH form)\",\n );\n }\n return { ok: reasons.length === 0, reasons };\n}\n\nexport interface GthParsedEntry {\n element: string;\n potentialName: string;\n aliases: string[];\n nElec: number[];\n rLoc: number;\n nexpPpl: number;\n cexpPpl: number[];\n nprj: number;\n channels: Array<{\n r: number;\n nprjPpnl: number;\n hprj: number[][];\n }>;\n hasKprj: boolean;\n kprj?: number[][][];\n}\n\n/* True for comment / blank / entry-boundary lines vs numeric data lines. /\nfunction isBoundaryLine(line: string \| undefined): boolean {\n if (line === undefined) return true;\n const t = line.trim();\n return t === \"\" \|\| t.startsWith(\"#\") \|\| !/^[-+.\\d]/.test(t);\n}\n\n/\n Expand upper-triangle values (row-major: h11, h12, ..., h1n, h22, ...)\n * into a full symmetric n×n matrix, matching GthData's [channel][i][j].\n /\nfunction upperToSymmetric(flat: number[], n: number): number[][] {\n const m: number[][] = [];\n for (let i = 0; i < n; i++) m.push(new Array(n).fill(0));\n let pos = 0;\n for (let i = 0; i < n; i++) {\n for (let j = i; j < n; j++) {\n const v = flat[pos++] ?? 0;\n m[i][j] = v;\n m[j][i] = v;\n }\n }\n return m;\n}\n\n/\n Parse a monolithic GTH_POTENTIALS file into individual element entries.\n /\nexport function parseGTHFile(text: string): GthParsedEntry[] {\n const entries: GthParsedEntry[] = [];\n const lines = text.split(\"\\n\");\n let i = 0;\n\n while (i < lines.length) {\n const line = lines[i].trim();\n\n // Skip comment lines and blank lines\n if (line.startsWith(\"#\") \|\| line === \"\") {\n i++;\n continue;\n }\n\n // This should be an element header line\n const headerParts = line.split(/\\s+/);\n if (headerParts.length < 2) {\n i++;\n continue;\n }\n\n const element = headerParts[0];\n const potentialName = headerParts[1] ?? \"\";\n const aliases = headerParts.slice(2);\n i++;\n\n // Skip comment lines between entries\n while (i < lines.length && (lines[i].trim().startsWith(\"#\") \|\| lines[i].trim() === \"\")) {\n i++;\n }\n\n if (i >= lines.length) break;\n\n // Valence electron configuration\n const nElec = lines[i++].trim().split(/\\s+/).map(Number);\n\n // Local part\n const localParts = lines[i++].trim().split(/\\s+/);\n const rLoc = parseFortranNumber(localParts[0]);\n const nexpPpl = parseInt(localParts[1]);\n const cexpPpl: number[] = [];\n for (let k = 0; k < nexpPpl; k++) {\n cexpPpl.push(parseFortranNumber(localParts[2 + k]));\n }\n\n // Number of non-local projector channels\n const nprj = parseInt(lines[i++].trim());\n\n // Non-local projector channels\n const channels: GthParsedEntry[\"channels\"] = [];\n let hasKprj = false;\n const kprjArrays: number[][][] = [];\n\n for (let l = 0; l < nprj && i < lines.length; l++) {\n const channelParts = lines[i++].trim().split(/\\s+/);\n const r = parseFortranNumber(channelParts[0]);\n const nprjPpnl = parseInt(channelParts[1]);\n\n // Upper-triangle size of the h-matrix for this channel.\n const hNeeded = (nprjPpnl (nprjPpnl + 1)) / 2;\n\n // Read h-matrix: inline tokens first, then one value per following line.\n const hFlat: number[] = [];\n let inlineIdx = 2;\n while (hFlat.length < hNeeded) {\n if (inlineIdx < channelParts.length) {\n hFlat.push(parseFortranNumber(channelParts[inlineIdx++]));\n } else if (i < lines.length) {\n hFlat.push(parseFortranNumber(lines[i++].trim().split(/\\s+/)[0]));\n } else {\n hFlat.push(0);\n }\n }\n const hprj: number[][] = upperToSymmetric(hFlat, nprjPpnl);\n\n channels.push({ r, nprjPpnl, hprj });\n\n // k-matrix (SOC): inline remainder on the channel line, if present.\n const inlineRemainder = channelParts.slice(inlineIdx).map(parseFortranNumber);\n if (\n !hasKprj &&\n inlineRemainder.length >= hNeeded &&\n inlineRemainder.every(Number.isFinite)\n ) {\n hasKprj = true;\n const kFlat = inlineRemainder.slice(0, hNeeded);\n const kmat = upperToSymmetric(kFlat, nprjPpnl);\n while (kprjArrays.length < l) kprjArrays.push([]);\n kprjArrays.push(kmat);\n } else if (!hasKprj && l === nprj - 1 && hNeeded > 0) {\n // Trailing multi-line k block: only valid on the LAST channel, where\n // the lines after it must be an entry boundary (not next-channel data).\n const kFlat: number[] = [];\n let j = i;\n while (kFlat.length < hNeeded && j < lines.length && !isBoundaryLine(lines[j])) {\n kFlat.push(parseFortranNumber(lines[j].trim().split(/\\s+/)[0]));\n j++;\n }\n if (kFlat.length === hNeeded && isBoundaryLine(lines[j])) {\n hasKprj = true;\n i = j;\n const kmat = upperToSymmetric(kFlat, nprjPpnl);\n while (kprjArrays.length < l) kprjArrays.push([]);\n kprjArrays.push(kmat);\n }\n }\n }\n\n entries.push({\n element,\n potentialName,\n aliases,\n nElec,\n rLoc,\n nexpPpl,\n cexpPpl,\n nprj,\n channels,\n hasKprj,\n kprj: hasKprj ? kprjArrays : undefined,\n });\n }\n\n return entries;\n}\n\n/*\n Evaluate the GTH local potential on a radial grid.\n \n V_local(r) = -Zval/r * erf(r / (sqrt(2) * r_loc))\n * + exp(-r²/(2r_loc²)) * (c0 + c1(r/r_loc)² + c2(r/r_loc)⁴ + c3(r/r_loc)⁶)\n \n * Units follow the units of cexpPpl (converted to Ry before calling).\n /\nfunction evalGthLocal(r: Float64Array, zVal: number, rLoc: number, cexpPpl: number[]): Float64Array {\n const vloc = new Float64Array(r.length);\n const c = [0, 0, 0, 0];\n for (let k = 0; k < cexpPpl.length && k < 4; k++) {\n c[k] = cexpPpl[k];\n }\n\n for (let i = 0; i < r.length; i++) {\n const ri = r[i];\n if (ri < 1e-15) {\n // At r=0, use L'Hopital: V_local(0) = -2Zval/(sqrt(2pi)rLoc) + c[0]\n vloc[i] = -2 * zVal / (Math.sqrt(2 * Math.PI) * rLoc) + c[0];\n continue;\n }\n\n const t = ri / rLoc;\n const t2 = t * t;\n const erfArg = ri / (Math.sqrt(2) * rLoc);\n const erfVal = erf(erfArg);\n const gauss = Math.exp(-t2 / 2);\n\n const coulomb = (-zVal / ri) * erfVal;\n const gaussian = gauss * (c[0] + c[1] * t2 + c[2] * t2 * t2 + c[3] * t2 * t2 * t2);\n\n vloc[i] = coulomb + gaussian;\n }\n\n return vloc;\n}\n\n/*\n Evaluate a GTH projector on a radial grid.\n \n \|r_{l,i}> = N * r^(l+2i-1) * exp(-r²/(2r_l²))\n /\nfunction evalGthProjector(\n r: Float64Array,\n l: number,\n i: number,\n rL: number,\n): Float64Array {\n const beta = new Float64Array(r.length);\n const exponent = l + 2 (i + 1) - 1;\n\n // Normalization constant\n const norm = Math.sqrt(2) * Math.pow(2 / (rL * rL), exponent + 0.5) /\n Math.sqrt(gamma(exponent + 0.5));\n\n for (let k = 0; k < r.length; k++) {\n const ri = r[k];\n if (ri < 1e-15) {\n beta[k] = exponent === 0 ? norm : 0;\n } else {\n beta[k] = norm * Math.pow(ri, exponent) * Math.exp(-ri * ri / (2 * rL * rL));\n }\n }\n\n return beta;\n}\n\n/*\n Parse a single GTH/HGH entry and convert to a first-class Pseudopotential.\n /\nexport function fromGTH(text: string): Pseudopotential {\n const entries = parseGTHFile(text);\n if (entries.length === 0) {\n throw new Error(\"No GTH entries found in file\");\n }\n return fromGthEntry(entries[0]);\n}\n\n/\n Parse a single GTH entry into a first-class Pseudopotential.\n \n Analytical parameters are converted to Ry and stored in `gth` alongside\n * an evaluated tabulation on a logarithmic grid.\n /\nexport function fromGthEntry(entry: GthParsedEntry): Pseudopotential {\n const zVal = entry.nElec.reduce((a, b) => a + b, 0);\n const lMax = entry.channels.length > 0 ? entry.channels.length - 1 : 0;\n\n const format: PseudopotentialFormat = /HGH/i.test(entry.potentialName)\n ? \"HGH\"\n : \"GTH\";\n\n // Build a logarithmic radial grid\n const npts = 500;\n const rmax = 20.0; // Bohr, sufficient for most pseudopotentials\n const { r, rab } = makeRadialGrid({ npts, rmax, type: \"log\" });\n\n // Convert analytical energies Hartree → Ry.\n const cexpPplRy = entry.cexpPpl.map(haToRy);\n const hprjRy = entry.channels.map((ch) =>\n ch.hprj.map((row) => row.map(haToRy)),\n );\n const kprjRy = entry.kprj?.map((m) => m.map((row) => row.map(haToRy)));\n\n // Evaluate local potential (Ry)\n const localVloc = evalGthLocal(r, zVal, entry.rLoc, cexpPplRy);\n\n // Evaluate projectors (normalization is unit-free)\n const betas: BetaProjector[] = [];\n const dij: Array<[number, number, number]> = [];\n let projIdx = 1;\n\n for (let l = 0; l < entry.channels.length; l++) {\n const ch = entry.channels[l];\n for (let p = 0; p < ch.nprjPpnl; p++) {\n const betaData = evalGthProjector(r, l, p, ch.r);\n betas.push({\n index: projIdx + p,\n angularMomentum: l,\n ultrasoftCutoffRadius: 0,\n label: `${l}${\"spdf\"[l] ?? l}${p + 1}`,\n beta: betaData,\n });\n }\n // D_ij is the full h-block: for GTH the h-matrix couples the\n // projectors of a channel directly.\n for (let p = 0; p < ch.nprjPpnl; p++) {\n for (let q = 0; q < ch.nprjPpnl; q++) {\n dij.push([projIdx + p, projIdx + q, hprjRy[l]?.[p]?.[q] ?? (p === q ? 1.0 : 0)]);\n }\n }\n projIdx += ch.nprjPpnl;\n }\n\n const mesh: PseudopotentialMesh = {\n gridType: \"logarithmic\",\n rmax,\n r,\n rab,\n };\n\n // GTH analytical data (energies in Ry)\n const gthData: GthData = {\n nElec: entry.nElec,\n rLoc: entry.rLoc,\n cexpPpl: cexpPplRy,\n rPs: entry.channels.map((ch) => ch.r),\n hprj: hprjRy,\n kprj: kprjRy,\n };\n\n const header: PseudopotentialHeader = {\n element: entry.element,\n pseudoType: \"NC\",\n relativistic: \"scalar\",\n isUltrasoft: false,\n isPaw: false,\n isCoulomb: false,\n hasSo: entry.hasKprj,\n hasWfc: false,\n hasGipaw: false,\n pawAsGipaw: false,\n coreCorrection: false,\n functional: entry.potentialName,\n zValence: zVal,\n totalPsenergy: 0,\n wfcCutoff: 0,\n rhoCutoff: 0,\n lMax,\n lMaxRho: lMax,\n lLocal: 0,\n meshSize: npts,\n numberOfWfc: 0,\n numberOfProj: betas.length,\n };\n\n return {\n format,\n units: { ...CANONICAL_UNITS },\n provenance: {\n sourceFormat: format,\n analytical: true,\n notes:\n entry.aliases.length > 0 ? `aliases: ${entry.aliases.join(\", \")}` : undefined,\n },\n header,\n mesh,\n local: { vloc: localVloc } satisfies PseudopotentialLocal,\n nonlocal: { betas, dij } satisfies PseudopotentialNonlocal,\n pswfc: [],\n rhoatom: new Float64Array(npts),\n gth: gthData,\n };\n}\n\n/\n Serialize a first-class Pseudopotential to GTH format (single element entry).\n * Analytical parameters are written back in Hartree (native GTH units);\n * the k-matrix is written inline on the channel line when present.\n /\nexport function toGTH(pp: Pseudopotential): string {\n const check = canWriteGTH(pp);\n if (!pp.gth) {\n throw new Error(check.reasons[0]);\n }\n\n const lines: string[] = [];\n const gth = pp.gth;\n\n lines.push(`# ${pp.header.element} ${pp.header.functional}`);\n lines.push(`# Element symbol Name of the potential Alias names`);\n lines.push(`# n_elec(s) n_elec(p) n_elec(d) ...`);\n lines.push(`# r_loc nexp_ppl cexp_ppl(1) ... cexp_ppl(nexp_ppl)`);\n lines.push(`# nprj`);\n lines.push(`${pp.header.element} ${pp.header.functional}`);\n\n // Valence electron configuration\n let nElec: number[];\n if (gth.nElec && gth.nElec.length > 0) {\n nElec = [...gth.nElec];\n } else {\n // Estimate from betas\n nElec = new Array(pp.header.lMax + 1).fill(0);\n for (const beta of pp.nonlocal.betas) {\n nElec[beta.angularMomentum] = Math.max(nElec[beta.angularMomentum], 1);\n }\n if (nElec[0] === 0) nElec[0] = Math.round(pp.header.zValence);\n }\n lines.push(nElec.join(\" \"));\n\n // Local part (Ry → Ha)\n const cHa = gth.cexpPpl.map((c) => c RY_TO_HA);\n lines.push(`${formatFortranNumber(gth.rLoc)} ${cHa.length} ${cHa.map((c) => formatFortranNumber(c)).join(\" \")}`);\n\n // Non-local part (Ry → Ha)\n lines.push(`${gth.rPs.length}`);\n for (let l = 0; l < gth.hprj.length; l++) {\n const h = gth.hprj[l];\n const nprj = h.length;\n // An empty padding entry (no k data for this channel) takes the legacy\n // layout; only channels with actual k values go inline.\n const k = gth.kprj?.[l];\n if (k && k.length > 0) {\n // k-matrix inline on the channel line so the parser recovers it.\n const hVals: string[] = [];\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n hVals.push(formatFortranNumber((h[i]?.[j] ?? 0) * RY_TO_HA));\n }\n }\n const kVals: string[] = [];\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n kVals.push(formatFortranNumber((k[i]?.[j] ?? 0) * RY_TO_HA));\n }\n }\n lines.push(\n `${formatFortranNumber(gth.rPs[l])} ${nprj} ${hVals.join(\" \")} ${kVals.join(\" \")}`,\n );\n } else {\n lines.push(`${formatFortranNumber(gth.rPs[l])} ${nprj}`);\n // h-matrix upper triangle\n for (let i = 0; i < nprj; i++) {\n for (let j = i; j < nprj; j++) {\n const val = (h[i]?.[j] ?? 0) * RY_TO_HA;\n lines.push(formatFortranNumber(val));\n }\n }\n }\n }\n\n return lines.join(\"\\n\");\n}\n\n// Simple error function approximation (Abramowitz & Stegun)\nfunction erf(x: number): number {\n const a1 = 0.254829592;\n const a2 = -0.284496736;\n const a3 = 1.421413741;\n const a4 = -1.453152027;\n const a5 = 1.061405429;\n const p = 0.3275911;\n\n const sign = x >= 0 ? 1 : -1;\n const absX = Math.abs(x);\n const t = 1.0 / (1.0 + p * absX);\n const y = 1.0 - (((((a5 * t + a4) * t) + a3) * t + a2) * t + a1) * t * Math.exp(-absX * absX);\n\n return sign * y;\n}\n\n// Gamma function approximation (Stirling + Lanczos for small arguments)\nfunction gamma(z: number): number {\n if (z < 0.5) {\n return Math.PI / (Math.sin(Math.PI * z) * gamma(1 - z));\n }\n z -= 1;\n const g = 7;\n const c = [\n 0.99999999999980993,\n 676.5203681218851,\n -1259.1392167224028,\n 771.32342877765313,\n -176.61502916214059,\n 12.507343278686905,\n -0.13857109526572012,\n 9.9843695780195716e-6,\n 1.5056327351493116e-7,\n ];\n let x = c[0];\n for (let i = 1; i < g + 2; i++) {\n x += c[i] / (z + i);\n }\n const t = z + g + 0.5;\n return Math.sqrt(2 * Math.PI) * Math.pow(t, z + 0.5) * Math.exp(-t) * x;\n}\n","/*\n Unified entry point for pseudopotential I/O.\n \n Every format adapter converts between text and the first-class\n * Pseudopotential object. This registry adds format detection plus\n * `parse` / `serialize` / `convert` dispatch so callers never need to know\n * which adapter to use.\n /\n\nimport type { Pseudopotential, PseudopotentialFormat } from \"../../pseudopotential/pseudopotential\";\n\nimport { fromUPF, toUPF } from \"./upf\";\nimport { fromUPFv1, toUPFv1 } from \"./upf-v1\";\nimport { fromPSP8, toPSP8, canWritePSP8 } from \"./psp8\";\nimport { fromPSML, toPSML, canWritePSML } from \"./psml\";\nimport { fromFHI, toFHI, canWriteFHI } from \"./fhi\";\nimport { fromGTH, toGTH, canWriteGTH } from \"./gth\";\n\n/* Non-empty lines of a text, for header sniffing. /\nfunction nonEmptyLines(text: string): string[] {\n return text.split(\"\\n\").filter((l) => l.trim().length > 0);\n}\n\n/\n Detect the pseudopotential format of a text buffer.\n \n Heuristics (first match wins):\n * - `<psml` tag → PSML\n * - `<UPF` root → UPF2\n * - `<PP_HEADER>` without `<UPF` → UPF1\n * - element + GTH/HGH header line → GTH\n * - pspcod=8 header line → PSP8\n * - FHI title / numeric lead → CPI (fromFHI auto-detects .fhi vs .cpi)\n \n @throws If no known format signature is found.\n /\nexport function detectFormat(text: string): PseudopotentialFormat {\n // Root-tag checks run on the file head only: these tags always open their\n // documents, and full-text regex scans dominate detection cost on\n // multi-MB PAW files.\n const head = text.slice(0, 4096);\n if (/<psml[\\s>]/i.test(head)) return \"PSML\";\n if (/<UPF[\\s>]/.test(head)) return \"UPF2\";\n if (/<PP_HEADER>/.test(head)) return \"UPF1\";\n\n const lines = nonEmptyLines(text);\n if (lines.length === 0) throw new Error(\"Cannot detect format of empty input\");\n\n // First content line (skipping #-comments, which lead GTH files and our\n // own serializer output).\n const content = lines.filter((l) => !l.trim().startsWith(\"#\"));\n const first = (content[0] ?? lines[0]).trim();\n if (/^[A-Z][a-z]?\\s+\\SHGH/i.test(first)) return \"HGH\";\n if (/^[A-Z][a-z]?\\s+\\S(GTH\|HGH)/i.test(first)) return \"GTH\";\n\n if (lines.length >= 3 && /^\\s8\\s+\\d+/.test(lines[2])) return \"PSP8\";\n\n if (\n /fhi98\|troullier\|martins\|pspdat/i.test(first) \|\|\n (/fhi/i.test(text.slice(0, 500)) && lines.length > 7 && /^\\s\\d/.test(lines[7] ?? \"\"))\n ) {\n return \"CPI\";\n }\n\n if (/^\\s[-+.\\d]/.test(first)) return \"CPI\";\n\n throw new Error(\"Unknown pseudopotential format: no recognized signature\");\n}\n\n/*\n Parse pseudopotential text into a first-class Pseudopotential object.\n * The format is auto-detected unless explicitly given.\n /\nexport function parse(\n text: string,\n format?: PseudopotentialFormat,\n): Pseudopotential {\n const fmt = format ?? detectFormat(text);\n switch (fmt) {\n case \"UPF2\":\n return fromUPF(text);\n case \"UPF1\":\n return fromUPFv1(text);\n case \"PSP8\":\n return fromPSP8(text);\n case \"PSML\":\n return fromPSML(text);\n case \"CPI\":\n return fromFHI(text);\n case \"GTH\":\n case \"HGH\":\n return fromGTH(text);\n default:\n throw new Error(`Unsupported pseudopotential format: ${fmt as string}`);\n }\n}\n\n/\n Serialize a first-class Pseudopotential to the requested format\n * (default UPF2, the lossless superset).\n /\nexport function serialize(\n pp: Pseudopotential,\n format: PseudopotentialFormat = \"UPF2\",\n): string {\n switch (format) {\n case \"UPF2\":\n return toUPF(pp);\n case \"UPF1\":\n return toUPFv1(pp);\n case \"PSP8\":\n return toPSP8(pp);\n case \"PSML\":\n return toPSML(pp);\n case \"CPI\":\n return toFHI(pp);\n case \"GTH\":\n case \"HGH\":\n return toGTH(pp);\n default:\n throw new Error(`Unsupported pseudopotential format: ${format as string}`);\n }\n}\n\n/\n Convert pseudopotential text from its (auto-detected) source format to a\n * target format. Lossy conversions (e.g. PAW → PSP8) produce best-effort\n * output; check `canSerialize()` first for safety.\n /\nexport function convert(\n text: string,\n target: PseudopotentialFormat,\n source?: PseudopotentialFormat,\n): string {\n return serialize(parse(text, source), target);\n}\n\nexport interface SerializationCheck {\n ok: boolean;\n reasons: string[];\n}\n\n/\n Report whether a first-class pseudopotential can be faithfully written to\n * the requested format. UPF2 (the superset) is always safe.\n /\nexport function canSerialize(\n pp: Pseudopotential,\n format: PseudopotentialFormat,\n): SerializationCheck {\n switch (format) {\n case \"UPF2\":\n case \"UPF1\":\n return { ok: true, reasons: [] };\n case \"PSP8\":\n return canWritePSP8(pp);\n case \"PSML\":\n return canWritePSML(pp);\n case \"CPI\":\n return canWriteFHI(pp);\n case \"GTH\":\n case \"HGH\":\n return canWriteGTH(pp);\n default:\n return { ok: false, reasons: [`unknown format ${(format as string) ?? \"\"}`] };\n }\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\n/* Serializes a Structure to a JSON-serializable object. /\nexport function toJSON(structure: Structure) {\n return {\n lattice: Array.from(structure.lattice.basis.data),\n sites: structure.sites.map((s) => ({\n species: s.species,\n frac: Array.from(s.frac),\n })),\n };\n}\n\n/* Deserializes a Structure from a JSON object. /\nexport function fromJSON(data: any): Structure {\n return {\n lattice: createLattice(data.lattice),\n sites: data.sites.map((s: any) => ({\n species: s.species,\n frac: new Float64Array(s.frac),\n })),\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\n\nimport { cartesian } from \"../site/cartesian\";\nimport { fractional } from \"../site/fractional\";\n\nimport {\n AtomicNumberToSymbol,\n SymbolToAtomicNumber,\n} from \"@/core/data/periodictable\";\n\n/* A numpy-style serialized ndarray as produced by ASE's JSON encoder. /\ninterface ASEndarray {\n __ndarray__: [number[], string, Array<number \| boolean>];\n}\n\n/* An ASE `Atoms` object serialized through ase.io.jsonio.write_json. /\nexport interface ASEAtoms {\n numbers: ASEndarray;\n positions: ASEndarray;\n cell: ASEndarray;\n pbc: ASEndarray;\n __ase_objtype__: \"atoms\";\n [key: string]: unknown;\n}\n\nfunction decodeNdarray(obj: ASEndarray): Array<number \| boolean> {\n return obj.__ndarray__[2];\n}\n\nfunction encodeNdarray(\n shape: number[],\n dtype: string,\n data: Array<number \| boolean>,\n): ASEndarray {\n return { __ndarray__: [shape, dtype, data] };\n}\n\n/* Deserializes an ASE `Atoms` JSON object into a Structure.\n \n ASE stores Cartesian positions and atomic numbers; these are converted into\n * the library's fractional-coordinate representation using the supplied cell. /\nexport function fromASE(data: ASEAtoms): Structure {\n const cellFlat = decodeNdarray(data.cell) as number[];\n const lattice = createLattice(new Float64Array(cellFlat));\n\n const positions = decodeNdarray(data.positions) as number[];\n const numbers = decodeNdarray(data.numbers) as number[];\n\n const n = numbers.length;\n const sites = new Array(n);\n\n for (let i = 0; i < n; i++) {\n const z = numbers[i];\n const symbol = AtomicNumberToSymbol.get(z);\n\n if (symbol === undefined) {\n throw new Error(`Unknown atomic number ${z}`);\n }\n\n const cart = new Float64Array([\n positions[3 i],\n positions[3 * i + 1],\n positions[3 * i + 2],\n ]);\n\n const frac = fractional(lattice, cart);\n\n sites[i] = {\n species: { symbol },\n frac,\n };\n }\n\n const out: Structure & { pbc?: boolean[] } = { lattice, sites };\n\n const pbc = decodeNdarray(data.pbc) as boolean[];\n if (pbc.some((v) => !v)) {\n out.pbc = [pbc[0], pbc[1], pbc[2]];\n }\n\n return out;\n}\n\n/** Serializes a Structure to an ASE `Atoms` JSON object. /\nexport function toASE(structure: Structure): ASEAtoms {\n const m = structure.lattice.basis.data;\n\n const n = structure.sites.length;\n const positions = new Array<number>(n 3);\n const numbers = new Array<number>(n);\n\n for (let i = 0; i < n; i++) {\n const site = structure.sites[i];\n\n const cart = cartesian(structure.lattice, site);\n positions[3 * i] = cart[0];\n positions[3 * i + 1] = cart[1];\n positions[3 * i + 2] = cart[2];\n\n const z = SymbolToAtomicNumber.get(site.species.symbol);\n\n if (z === undefined) {\n throw new Error(`Unknown element symbol ${site.species.symbol}`);\n }\n\n numbers[i] = z;\n }\n\n const pbc: boolean[] =\n (structure as Structure & { pbc?: boolean[] }).pbc ??\n [true, true, true];\n\n return {\n numbers: encodeNdarray([n], \"int64\", numbers),\n positions: encodeNdarray([n, 3], \"float64\", positions),\n cell: encodeNdarray([3, 3], \"float64\", Array.from(m)),\n pbc: encodeNdarray([3], \"bool\", pbc),\n __ase_objtype__: \"atoms\",\n };\n}\n","import { Structure } from \"../structure/structure\";\nimport { createLattice } from \"../lattice/lattice\";\nimport { volume } from \"../lattice/volume\";\nimport { parameters } from \"../lattice/parameters\";\n\nimport { cartesian } from \"../site/cartesian\";\n\n/** A single pymatgen species entry (an element with occupancy). /\nexport interface PymatgenSpecies {\n element: string;\n occu: number;\n}\n\n/* A pymatgen lattice block. /\nexport interface PymatgenLattice {\n matrix: number[][];\n pbc?: boolean[];\n a?: number;\n b?: number;\n c?: number;\n alpha?: number;\n beta?: number;\n gamma?: number;\n volume?: number;\n [key: string]: unknown;\n}\n\n/* A pymatgen site block. /\nexport interface PymatgenSite {\n species: PymatgenSpecies[];\n abc: [number, number, number] \| number[];\n properties?: Record<string, unknown>;\n label?: string;\n xyz?: [number, number, number] \| number[];\n [key: string]: unknown;\n}\n\n/* A pymatgen `Structure` serialized via `Structure.to(fmt=\"json\")`. /\nexport interface PymatgenStructure {\n \"@module\": string;\n \"@class\": string;\n charge?: number;\n lattice: PymatgenLattice;\n properties?: Record<string, unknown>;\n sites: PymatgenSite[];\n [key: string]: unknown;\n}\n\nfunction flattenMatrix(matrix: number[][]): number[] {\n const out: number[] = [];\n\n for (const row of matrix) {\n for (const v of row) {\n out.push(v);\n }\n }\n\n return out;\n}\n\n/* Deserializes a pymatgen `Structure` JSON object into a Structure. /\nexport function fromPymatgen(data: PymatgenStructure): Structure {\n const lattice = createLattice(new Float64Array(flattenMatrix(data.lattice.matrix)));\n\n const sites = data.sites.map((site) => {\n const primary = site.species[0];\n\n if (primary === undefined) {\n throw new Error(\"Site has no species\");\n }\n\n const label = site.label ?? primary.element;\n\n return {\n species: {\n symbol: primary.element,\n properties: { occu: primary.occu, label },\n },\n\n frac: new Float64Array(site.abc),\n };\n });\n\n const out: Structure & { charge?: number; properties?: unknown } = {\n lattice,\n sites,\n };\n\n if (data.charge !== undefined) {\n out.charge = data.charge;\n }\n\n if (data.properties !== undefined) {\n out.properties = data.properties;\n }\n\n return out;\n}\n\n/* Serializes a Structure to a pymatgen `Structure` JSON object. /\nexport function toPymatgen(structure: Structure): PymatgenStructure {\n const m = structure.lattice.basis.data;\n\n const matrix = [\n [m[0], m[1], m[2]],\n [m[3], m[4], m[5]],\n [m[6], m[7], m[8]],\n ];\n\n const [a, b, c, alpha, beta, gamma] = parameters(structure.lattice);\n\n const sites = structure.sites.map((site) => {\n const props = site.species.properties ?? {};\n\n const label = (props.label as string) ?? site.species.symbol;\n const occu = (props.occu as number) ?? 1;\n\n const cart = cartesian(structure.lattice, site);\n\n return {\n species: [{ element: site.species.symbol, occu }],\n abc: Array.from(site.frac),\n properties: {},\n label,\n xyz: Array.from(cart),\n };\n });\n\n return {\n \"@module\": \"pymatgen.core.structure\",\n \"@class\": \"Structure\",\n charge: (structure as Structure & { charge?: number }).charge ?? 0.0,\n lattice: {\n matrix,\n pbc: [true, true, true],\n a,\n b,\n c,\n alpha,\n beta,\n gamma,\n volume: volume(structure.lattice),\n },\n properties:\n (structure as Structure & { properties?: Record<string, unknown> })\n .properties ?? {},\n sites,\n };\n}\n","/\n Validation for first-class pseudopotential objects.\n \n `validate()` returns a list of human-readable issues (empty = valid).\n * Structural mismatches (wrong array lengths, out-of-range D_ij indices) are\n * the main target; physical sanity (signs, cutoffs) is reported as warnings\n * with a \"warn:\" prefix.\n /\n\nimport type { Pseudopotential } from \"./pseudopotential\";\n\n/* Validate a pseudopotential object, returning a list of issue strings. /\nexport function validate(pp: Pseudopotential): string[] {\n const issues: string[] = [];\n const n = pp.mesh.r.length;\n\n if (n === 0) issues.push(\"mesh.r is empty\");\n if (pp.mesh.rab.length !== n) {\n issues.push(\n `mesh.rab length ${pp.mesh.rab.length} != mesh.r length ${n}`,\n );\n }\n if (pp.header.meshSize !== n) {\n issues.push(\n `header.meshSize ${pp.header.meshSize} != mesh.r length ${n}`,\n );\n }\n if (pp.local.vloc.length !== n) {\n issues.push(`local.vloc length ${pp.local.vloc.length} != mesh size ${n}`);\n }\n if (pp.rhoatom.length !== 0 && pp.rhoatom.length !== n) {\n issues.push(`rhoatom length ${pp.rhoatom.length} != mesh size ${n}`);\n }\n if (pp.nlcc && pp.nlcc.length !== n) {\n issues.push(`nlcc length ${pp.nlcc.length} != mesh size ${n}`);\n }\n\n const nBetas = pp.nonlocal.betas.length;\n if (pp.header.numberOfProj !== 0 && pp.header.numberOfProj !== nBetas) {\n issues.push(\n `header.numberOfProj ${pp.header.numberOfProj} != betas length ${nBetas}`,\n );\n }\n pp.nonlocal.betas.forEach((beta, i) => {\n if (beta.beta.length !== n) {\n issues.push(\n `beta[${i}] (l=${beta.angularMomentum}) length ${beta.beta.length} != mesh size ${n}`,\n );\n }\n });\n for (const [nb, mb, val] of pp.nonlocal.dij) {\n if (!Number.isInteger(nb) \|\| nb < 1 \|\| nb > nBetas) {\n issues.push(`dij entry [${nb}, ${mb}] has out-of-range nb=${nb}`);\n }\n if (!Number.isInteger(mb) \|\| mb < 1 \|\| mb > nBetas) {\n issues.push(`dij entry [${nb}, ${mb}] has out-of-range mb=${mb}`);\n }\n if (Number.isNaN(val)) issues.push(`dij entry [${nb}, ${mb}] is NaN`);\n }\n\n if (pp.header.numberOfWfc !== 0 && pp.header.numberOfWfc !== pp.pswfc.length) {\n issues.push(\n `header.numberOfWfc ${pp.header.numberOfWfc} != pswfc length ${pp.pswfc.length}`,\n );\n }\n pp.pswfc.forEach((wfc, i) => {\n if (wfc.chi.length !== n) {\n issues.push(`pswfc[${i}] chi length ${wfc.chi.length} != mesh size ${n}`);\n }\n });\n if (pp.semilocal) {\n pp.semilocal.forEach((sl, i) => {\n if (sl.vnl.length !== n) {\n issues.push(\n `semilocal[${i}] (l=${sl.l}) length ${sl.vnl.length} != mesh size ${n}`,\n );\n }\n });\n }\n if (pp.fullWfc) {\n pp.fullWfc.forEach((wfc, i) => {\n if (wfc.aewfc.length !== n) {\n issues.push(\n `fullWfc[${i}] aewfc length ${wfc.aewfc.length} != mesh size ${n}`,\n );\n }\n });\n }\n\n const aug = pp.nonlocal.augmentation;\n if (aug) {\n if (aug.q && aug.q.length === 0) issues.push(\"augmentation.q is empty\");\n if (aug.qijl) {\n aug.qijl.forEach((q, i) => {\n if (q.qijl.length !== n) {\n issues.push(\n `augmentation.qijl[${i}] (i=${q.i},j=${q.j},l=${q.l}) length ${q.qijl.length} != mesh size ${n}`,\n );\n }\n if (q.i < 1 \|\| q.i > nBetas \|\| q.j < 1 \|\| q.j > nBetas) {\n issues.push(\n `augmentation.qijl[${i}] references out-of-range projectors (i=${q.i},j=${q.j})`,\n );\n }\n });\n }\n }\n\n if (pp.paw) {\n if (pp.paw.aeVloc.length !== 0 && pp.paw.aeVloc.length !== n) {\n issues.push(`paw.aeVloc length ${pp.paw.aeVloc.length} != mesh size ${n}`);\n }\n if (pp.paw.aeNlcc.length !== 0 && pp.paw.aeNlcc.length !== n) {\n issues.push(`paw.aeNlcc length ${pp.paw.aeNlcc.length} != mesh size ${n}`);\n }\n }\n\n if (pp.units.energy !== \"Ry\" \|\| pp.units.length !== \"Bohr\") {\n issues.push(\n `warn: non-canonical units energy=${pp.units.energy} length=${pp.units.length}`,\n );\n }\n if (pp.header.isPaw && !pp.paw) {\n issues.push(\"warn: header.isPaw is set but paw data is missing\");\n }\n if (pp.header.hasSo && !pp.spinOrbit) {\n issues.push(\"warn: header.hasSo is set but spinOrbit data is missing\");\n }\n\n return issues;\n}\n","/\n Maps each International spacegroup number (1-230) to the list of possible\n * Hall numbers for that spacegroup.\n \n Source: Seto's Home Page\n * http://pmsl.planet.sci.kobe-u.ac.jp/~seto/?page_id=37&lang=en\n /\nexport const hallNumbersOfSpacegroup: Record<number, number[]> = {\n 1: [1],\n 2: [2],\n 3: [3, 4, 5],\n 4: [6, 7, 8],\n 5: [9, 10, 11, 12, 13, 14, 15, 16, 17],\n 6: [18, 19, 20],\n 7: [21, 22, 23, 24, 25, 26, 27, 28, 29],\n 8: [30, 31, 32, 33, 34, 35, 36, 37, 38],\n 9: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56],\n 10: [57, 58, 59],\n 11: [60, 61, 62],\n 12: [63, 64, 65, 66, 67, 68, 69, 70, 71],\n 13: [72, 73, 74, 75, 76, 77, 78, 79, 80],\n 14: [81, 82, 83, 84, 85, 86, 87, 88, 89],\n 15: [\n 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106,\n 107,\n ],\n 16: [108],\n 17: [109, 110, 111],\n 18: [112, 113, 114],\n 19: [115],\n 20: [116, 117, 118],\n 21: [119, 120, 121],\n 22: [122],\n 23: [123],\n 24: [124],\n 25: [125, 126, 127],\n 26: [128, 129, 130, 131, 132, 133],\n 27: [134, 135, 136],\n 28: [137, 138, 139, 140, 141, 142],\n 29: [143, 144, 145, 146, 147, 148],\n 30: [149, 150, 151, 152, 153, 154],\n 31: [155, 156, 157, 158, 159, 160],\n 32: [161, 162, 163],\n 33: [164, 165, 166, 167, 168, 169],\n 34: [170, 171, 172],\n 35: [173, 174, 175],\n 36: [176, 177, 178, 179, 180, 181],\n 37: [182, 183, 184],\n 38: [185, 186, 187, 188, 189, 190],\n 39: [191, 192, 193, 194, 195, 196],\n 40: [197, 198, 199, 200, 201, 202],\n 41: [203, 204, 205, 206, 207, 208],\n 42: [209, 210, 211],\n 43: [212, 213, 214],\n 44: [215, 216, 217],\n 45: [218, 219, 220],\n 46: [221, 222, 223, 224, 225, 226],\n 47: [227],\n 48: [228, 229],\n 49: [230, 231, 232],\n 50: [233, 234, 235, 236, 237, 238],\n 51: [239, 240, 241, 242, 243, 244],\n 52: [245, 246, 247, 248, 249, 250],\n 53: [251, 252, 253, 254, 255, 256],\n 54: [257, 258, 259, 260, 261, 262],\n 55: [263, 264, 265],\n 56: [266, 267, 268],\n 57: [269, 270, 271, 272, 273, 274],\n 58: [275, 276, 277],\n 59: [278, 279, 280, 281, 282, 283],\n 60: [284, 285, 286, 287, 288, 289],\n 61: [290, 291],\n 62: [292, 293, 294, 295, 296, 297],\n 63: [298, 299, 300, 301, 302, 303],\n 64: [304, 305, 306, 307, 308, 309],\n 65: [310, 311, 312],\n 66: [313, 314, 315],\n 67: [316, 317, 318, 319, 320, 321],\n 68: [322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333],\n 69: [334],\n 70: [335, 336],\n 71: [337],\n 72: [338, 339, 340],\n 73: [341, 342],\n 74: [343, 344, 345, 346, 347, 348],\n 75: [349],\n 76: [350],\n 77: [351],\n 78: [352],\n 79: [353],\n 80: [354],\n 81: [355],\n 82: [356],\n 83: [357],\n 84: [358],\n 85: [359, 360],\n 86: [361, 362],\n 87: [363],\n 88: [364, 365],\n 89: [366],\n 90: [367],\n 91: [368],\n 92: [369],\n 93: [370],\n 94: [371],\n 95: [372],\n 96: [373],\n 97: [374],\n 98: [375],\n 99: [376],\n 100: [377],\n 101: [378],\n 102: [379],\n 103: [380],\n 104: [381],\n 105: [382],\n 106: [383],\n 107: [384],\n 108: [385],\n 109: [386],\n 110: [387],\n 111: [388],\n 112: [389],\n 113: [390],\n 114: [391],\n 115: [392],\n 116: [393],\n 117: [394],\n 118: [395],\n 119: [396],\n 120: [397],\n 121: [398],\n 122: [399],\n 123: [400],\n 124: [401],\n 125: [402, 403],\n 126: [404, 405],\n 127: [406],\n 128: [407],\n 129: [408, 409],\n 130: [410, 411],\n 131: [412],\n 132: [413],\n 133: [414, 415],\n 134: [416, 417],\n 135: [418],\n 136: [419],\n 137: [420, 421],\n 138: [422, 423],\n 139: [424],\n 140: [425],\n 141: [426, 427],\n 142: [428, 429],\n 143: [430],\n 144: [431],\n 145: [432],\n 146: [433, 434],\n 147: [435],\n 148: [436, 437],\n 149: [438],\n 150: [439],\n 151: [440],\n 152: [441],\n 153: [442],\n 154: [443],\n 155: [444, 445],\n 156: [446],\n 157: [447],\n 158: [448],\n 159: [449],\n 160: [450, 451],\n 161: [452, 453],\n 162: [454],\n 163: [455],\n 164: [456],\n 165: [457],\n 166: [458, 459],\n 167: [460, 461],\n 168: [462],\n 169: [463],\n 170: [464],\n 171: [465],\n 172: [466],\n 173: [467],\n 174: [468],\n 175: [469],\n 176: [470],\n 177: [471],\n 178: [472],\n 179: [473],\n 180: [474],\n 181: [475],\n 182: [476],\n 183: [477],\n 184: [478],\n 185: [479],\n 186: [480],\n 187: [481],\n 188: [482],\n 189: [483],\n 190: [484],\n 191: [485],\n 192: [486],\n 193: [487],\n 194: [488],\n 195: [489],\n 196: [490],\n 197: [491],\n 198: [492],\n 199: [493],\n 200: [494],\n 201: [495, 496],\n 202: [497],\n 203: [498, 499],\n 204: [500],\n 205: [501],\n 206: [502],\n 207: [503],\n 208: [504],\n 209: [505],\n 210: [506],\n 211: [507],\n 212: [508],\n 213: [509],\n 214: [510],\n 215: [511],\n 216: [512],\n 217: [513],\n 218: [514],\n 219: [515],\n 220: [516],\n 221: [517],\n 222: [518, 519],\n 223: [520],\n 224: [521, 522],\n 225: [523],\n 226: [524],\n 227: [525, 526],\n 228: [527, 528],\n 229: [529],\n 230: [530],\n};\n","/\n Point group data: mapping, character tables, symmetry operations, and\n * optical activity labels for all 27 non-cubic crystallographic point groups.\n \n Rotation matrices are generated at runtime from axis/angle specs via\n * quaternion rotation (matching the Python/ASE Quaternion implementation).\n /\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\nexport type Vec3 = [number, number, number];\nexport type Matrix3x3 = [Vec3, Vec3, Vec3];\n/* Complex number as [real, imaginary]. /\nexport type Complex = [number, number];\n\n// Symmetry operation specs — declarative, not pre-computed\ninterface IdentityOp {\n type: \"I\";\n}\ninterface InversionOp {\n type: \"-I\";\n}\ninterface RotationOp {\n type: \"R\";\n axis: Vec3;\n angle: number;\n}\ninterface RotoreflectionOp {\n type: \"S\";\n axis: Vec3;\n angle: number;\n}\nexport type OpSpec = IdentityOp \| InversionOp \| RotationOp \| RotoreflectionOp;\n\nexport interface PointGroupEntry {\n classes: Record<number, OpSpec[]>;\n characterTable: Record<string, (number \| Complex)[]>;\n raman: string[];\n infrared: string[];\n hmSymbol: string;\n backscattering: string[][];\n}\n\n// ---------------------------------------------------------------------------\n// Matrix generation from OpSpec\n// ---------------------------------------------------------------------------\n\nconst TOL = 2 Number.EPSILON;\n\nexport function identity(): Matrix3x3 {\n return [\n [1, 0, 0],\n [0, 1, 0],\n [0, 0, 1],\n ];\n}\n\nexport function inversion(): Matrix3x3 {\n return [\n [-1, 0, 0],\n [0, -1, 0],\n [0, 0, -1],\n ];\n}\n\n/*\n Rotation matrix from axis and angle via quaternion.\n * Equivalent to ASE's Quaternion.rotation_matrix().\n /\nexport function rotationMatrix(axis: Vec3, angle: number): Matrix3x3 {\n const [ax, ay, az] = axis;\n const norm = Math.sqrt(ax ax + ay * ay + az * az);\n const half = angle / 2;\n const s = Math.sin(half) / norm;\n const c = Math.cos(half);\n // Quaternion [w, x, y, z]\n const qw = c;\n const qx = s * ax;\n const qy = s * ay;\n const qz = s * az;\n\n const raw: number[][] = [\n [\n 1 - 2 * (qy * qy + qz * qz),\n 2 * (qx * qy - qw * qz),\n 2 * (qx * qz + qw * qy),\n ],\n [\n 2 * (qx * qy + qw * qz),\n 1 - 2 * (qx * qx + qz * qz),\n 2 * (qy * qz - qw * qx),\n ],\n [\n 2 * (qx * qz - qw * qy),\n 2 * (qy * qz + qw * qx),\n 1 - 2 * (qx * qx + qy * qy),\n ],\n ];\n\n // Zero out near-zero entries (matches Python's tolerance logic)\n for (let i = 0; i < 3; i++) {\n for (let j = 0; j < 3; j++) {\n if (Math.abs(raw[i][j]) < TOL) raw[i][j] = 0;\n }\n }\n\n return raw as Matrix3x3;\n}\n\n/*\n Rotoreflection: rotation by angle + π, then negate (inversion).\n * Equivalent to Python's `rotoreflection(axis, angle) = -rotation(axis, angle + π)`.\n /\nexport function rotoreflectionMatrix(axis: Vec3, angle: number): Matrix3x3 {\n const m = rotationMatrix(axis, angle + Math.PI);\n return [\n [-m[0][0], -m[0][1], -m[0][2]],\n [-m[1][0], -m[1][1], -m[1][2]],\n [-m[2][0], -m[2][1], -m[2][2]],\n ];\n}\n\n/* Resolve an OpSpec to its concrete 3×3 matrix. /\nexport function resolveOp(op: OpSpec): Matrix3x3 {\n switch (op.type) {\n case \"I\":\n return identity();\n case \"-I\":\n return inversion();\n case \"R\":\n return rotationMatrix(op.axis, op.angle);\n case \"S\":\n return rotoreflectionMatrix(op.axis, op.angle);\n }\n}\n\n/* Resolve all operations in a class to their matrices. /\nexport function resolveClass(ops: OpSpec[]): Matrix3x3[] {\n return ops.map(resolveOp);\n}\n\n// ---------------------------------------------------------------------------\n// Common shorthand specs\n// ---------------------------------------------------------------------------\n\nconst I: IdentityOp = { type: \"I\" };\nconst NI: InversionOp = { type: \"-I\" };\n\nconst rz = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [0, 0, 1],\n angle,\n});\nconst rx = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [1, 0, 0],\n angle,\n});\nconst ry = (angle: number): RotationOp => ({\n type: \"R\",\n axis: [0, 1, 0],\n angle,\n});\nconst rAxis = (axis: Vec3, angle: number): RotationOp => ({\n type: \"R\",\n axis,\n angle,\n});\n\nconst sx = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [1, 0, 0],\n angle,\n});\nconst sy = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [0, 1, 0],\n angle,\n});\nconst sz = (angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis: [0, 0, 1],\n angle,\n});\nconst sAxis = (axis: Vec3, angle: number): RotoreflectionOp => ({\n type: \"S\",\n axis,\n angle,\n});\n\n// Frequently used irrational-containing axes\nconst SQRT3 = Math.sqrt(3);\nconst AX_N1_SQ3_0: Vec3 = [-1, SQRT3, 0];\nconst AX_N1_NSQ3_0: Vec3 = [-1, -SQRT3, 0];\nconst AX_SQ3_1_0: Vec3 = [SQRT3, 1, 0];\nconst AX_SQ3_N1_0: Vec3 = [SQRT3, -1, 0];\nconst AX_1_1_0: Vec3 = [1, 1, 0];\nconst AX_1_N1_0: Vec3 = [1, -1, 0];\n\n// Common angles\nconst PI = Math.PI;\nconst PI2 = PI / 2;\nconst PI3 = PI / 3;\nconst PI6 = PI / 6;\nconst TPI3 = (2 PI) / 3;\nconst NTPI3 = -(2 * PI) / 3;\nconst NPI3 = -PI / 3;\n\n// ---------------------------------------------------------------------------\n// Complex number constants (character table phase factors)\n// ---------------------------------------------------------------------------\n\n// w = exp(2πi/3), w2 = exp(-2πi/3)\nconst W: Complex = [-0.5, SQRT3 / 2];\nconst W2: Complex = [-0.5, -SQRT3 / 2];\nconst _1j: Complex = [0, 1];\nconst _1nj: Complex = [0, -1];\n\n// ---------------------------------------------------------------------------\n// International number ↔ HM/Schoenflies mapping\n// ---------------------------------------------------------------------------\n\nexport interface PGMapping {\n internationalNumber: number;\n hmSymbol: string;\n schoenflies: string;\n}\n\nexport const pointgroupMapping: PGMapping[] = [\n { internationalNumber: 0, hmSymbol: \"\", schoenflies: \"\" }, // placeholder for 1-indexing\n { internationalNumber: 1, hmSymbol: \"1\", schoenflies: \"C1\" },\n { internationalNumber: 2, hmSymbol: \"-1\", schoenflies: \"Ci\" },\n { internationalNumber: 3, hmSymbol: \"2\", schoenflies: \"C2\" },\n { internationalNumber: 4, hmSymbol: \"m\", schoenflies: \"Cs\" },\n { internationalNumber: 5, hmSymbol: \"2/m\", schoenflies: \"C2h\" },\n { internationalNumber: 6, hmSymbol: \"222\", schoenflies: \"D2\" },\n { internationalNumber: 7, hmSymbol: \"mm2\", schoenflies: \"C2v\" },\n { internationalNumber: 8, hmSymbol: \"mmm\", schoenflies: \"D2h\" },\n { internationalNumber: 9, hmSymbol: \"4\", schoenflies: \"C4\" },\n { internationalNumber: 10, hmSymbol: \"-4\", schoenflies: \"S4\" },\n { internationalNumber: 11, hmSymbol: \"4/m\", schoenflies: \"C4h\" },\n { internationalNumber: 12, hmSymbol: \"422\", schoenflies: \"D4\" },\n { internationalNumber: 13, hmSymbol: \"4mm\", schoenflies: \"C4v\" },\n { internationalNumber: 14, hmSymbol: \"-42m\", schoenflies: \"D2d\" },\n { internationalNumber: 15, hmSymbol: \"4/mmm\", schoenflies: \"D4h\" },\n { internationalNumber: 16, hmSymbol: \"3\", schoenflies: \"C3\" },\n { internationalNumber: 17, hmSymbol: \"-3\", schoenflies: \"C3i\" },\n { internationalNumber: 18, hmSymbol: \"32\", schoenflies: \"D3\" },\n { internationalNumber: 19, hmSymbol: \"3m\", schoenflies: \"C3v\" },\n { internationalNumber: 20, hmSymbol: \"-3m\", schoenflies: \"D3d\" },\n { internationalNumber: 21, hmSymbol: \"6\", schoenflies: \"C6\" },\n { internationalNumber: 22, hmSymbol: \"-6\", schoenflies: \"C3h\" },\n { internationalNumber: 23, hmSymbol: \"6/m\", schoenflies: \"C6h\" },\n { internationalNumber: 24, hmSymbol: \"622\", schoenflies: \"D6\" },\n { internationalNumber: 25, hmSymbol: \"6mm\", schoenflies: \"C6v\" },\n { internationalNumber: 26, hmSymbol: \"-6m2\", schoenflies: \"D3h\" },\n { internationalNumber: 27, hmSymbol: \"6/mmm\", schoenflies: \"D6h\" },\n // Cubic (kept for completeness, not used in layer analysis)\n { internationalNumber: 28, hmSymbol: \"23\", schoenflies: \"T\" },\n { internationalNumber: 29, hmSymbol: \"m-3\", schoenflies: \"Th\" },\n { internationalNumber: 30, hmSymbol: \"432\", schoenflies: \"O\" },\n { internationalNumber: 31, hmSymbol: \"-43m\", schoenflies: \"Td\" },\n { internationalNumber: 32, hmSymbol: \"m-3m\", schoenflies: \"Oh\" },\n];\n\n// ---------------------------------------------------------------------------\n// Point group dictionary — all 27 non-cubic groups\n// ---------------------------------------------------------------------------\n\nexport const pointgroupDict: Record<string, PointGroupEntry> = {\n // =======================================================================\n // TRICLINIC\n // =======================================================================\n\n C1: {\n classes: { 0: [I] },\n characterTable: { A: [1] },\n raman: [\"A\"],\n infrared: [\"A\"],\n hmSymbol: \"1\",\n backscattering: [[\"A\"], [\"A\"], [\"A\"]],\n },\n\n Ci: {\n classes: { 0: [I], 1: [NI] },\n characterTable: { Ag: [1, 1], Au: [1, -1] },\n raman: [\"Ag\"],\n infrared: [\"Au\"],\n hmSymbol: \"-1\",\n backscattering: [[\"Ag\"], [\"Ag\"], [\"Ag\"]],\n },\n\n // =======================================================================\n // MONOCLINIC\n // =======================================================================\n\n C2: {\n classes: { 0: [I], 1: [rz(PI)] },\n characterTable: { A: [1, 1], B: [1, -1] },\n raman: [\"A\", \"B\"],\n infrared: [\"A\", \"B\"],\n hmSymbol: \"2\",\n backscattering: [[\"A\", \"B\"], [\"A\", \"B\"], [\"A\"]],\n },\n\n Cs: {\n classes: { 0: [I], 1: [sz(0)] },\n characterTable: { \"A'\": [1, 1], \"A''\": [1, -1] },\n raman: [\"A'\", \"A''\"],\n infrared: [\"A'\", \"A''\"],\n hmSymbol: \"m\",\n backscattering: [[\"A'\", \"A''\"], [\"A'\", \"A''\"], [\"A'\"]],\n },\n\n C2h: {\n classes: { 0: [I], 1: [rz(PI)], 2: [NI], 3: [sz(0)] },\n characterTable: {\n Ag: [1, 1, 1, 1],\n Bg: [1, -1, 1, -1],\n Au: [1, 1, -1, -1],\n Bu: [1, -1, -1, 1],\n },\n raman: [\"Ag\", \"Bg\"],\n infrared: [\"Au\", \"Bu\"],\n hmSymbol: \"2/m\",\n backscattering: [[\"Ag\", \"Bg\"], [\"Ag\", \"Bg\"], [\"Ag\"]],\n },\n\n // =======================================================================\n // ORTHORHOMBIC\n // =======================================================================\n\n D2: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [ry(PI)],\n 3: [rx(PI)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B1: [1, 1, -1, -1],\n B2: [1, -1, 1, -1],\n B3: [1, -1, -1, 1],\n },\n raman: [\"A\", \"B1\", \"B2\", \"B3\"],\n infrared: [\"B1\", \"B2\", \"B3\"],\n hmSymbol: \"222\",\n backscattering: [\n [\"A\", \"B3\"],\n [\"A\", \"B2\"],\n [\"A\", \"B1\"],\n ],\n },\n\n C2v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sy(0)],\n 3: [sx(0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1],\n A2: [1, 1, -1, -1],\n B1: [1, -1, 1, -1],\n B2: [1, -1, -1, 1],\n },\n raman: [\"A1\", \"A2\", \"B1\", \"B2\"],\n infrared: [\"A1\", \"B1\", \"B2\"],\n hmSymbol: \"mm2\",\n backscattering: [\n [\"A1\", \"B2\"],\n [\"A1\", \"B1\"],\n [\"A1\", \"A2\"],\n ],\n },\n\n D2h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [ry(PI)],\n 3: [rx(PI)],\n 4: [NI],\n 5: [sz(0)],\n 6: [sy(0)],\n 7: [sx(0)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1],\n B1g: [1, 1, -1, -1, 1, 1, -1, -1],\n B2g: [1, -1, 1, -1, 1, -1, 1, -1],\n B3g: [1, -1, -1, 1, 1, -1, -1, 1],\n Au: [1, 1, 1, 1, -1, -1, -1, -1],\n B1u: [1, 1, -1, -1, -1, -1, 1, 1],\n B2u: [1, -1, 1, -1, -1, 1, -1, 1],\n B3u: [1, -1, -1, 1, -1, 1, 1, -1],\n },\n raman: [\"Ag\", \"B1g\", \"B2g\", \"B3g\"],\n infrared: [\"B1u\", \"B2u\", \"B3u\"],\n hmSymbol: \"mmm\",\n backscattering: [\n [\"Ag\", \"B3g\"],\n [\"Ag\", \"B2g\"],\n [\"Ag\", \"B1g\"],\n ],\n },\n\n // =======================================================================\n // TETRAGONAL\n // =======================================================================\n\n C4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2)],\n 3: [rz(-PI2)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B: [1, 1, -1, -1],\n \"1E\": [1, -1, _1nj, _1j],\n \"2E\": [1, -1, _1j, _1nj],\n },\n raman: [\"A\", \"B\", \"1E\", \"2E\"],\n infrared: [\"A\", \"1E\", \"2E\"],\n hmSymbol: \"4\",\n backscattering: [\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"B\"],\n ],\n },\n\n S4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sz(PI2)],\n 3: [sz(-PI2)],\n },\n characterTable: {\n A: [1, 1, 1, 1],\n B: [1, 1, -1, -1],\n \"1E\": [1, -1, _1nj, _1j],\n \"2E\": [1, -1, _1j, _1nj],\n },\n raman: [\"A\", \"B\", \"1E\", \"2E\"],\n infrared: [\"B\", \"1E\", \"2E\"],\n hmSymbol: \"-4\",\n backscattering: [\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"1E\", \"2E\", \"B\"],\n [\"A\", \"B\"],\n ],\n },\n\n C4h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2)],\n 3: [rz(-PI2)],\n 4: [NI],\n 5: [sz(0)],\n 6: [sz(-PI2)],\n 7: [sz(PI2)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1],\n Bg: [1, 1, -1, -1, 1, 1, -1, -1],\n \"1Eg\": [1, -1, _1nj, _1j, 1, -1, _1nj, _1j],\n \"2Eg\": [1, -1, _1j, _1nj, 1, -1, _1j, _1nj],\n Au: [1, 1, 1, 1, -1, -1, -1, -1],\n Bu: [1, 1, -1, -1, -1, -1, 1, 1],\n \"1Eu\": [1, -1, _1nj, _1j, -1, 1, _1j, _1nj],\n \"2Eu\": [1, -1, _1j, _1nj, -1, 1, _1nj, _1j],\n },\n raman: [\"Ag\", \"Bg\", \"1Eg\", \"2Eg\"],\n infrared: [\"Au\", \"1Eu\", \"2Eu\"],\n hmSymbol: \"4/m\",\n backscattering: [\n [\"Ag\", \"1Eg\", \"2Eg\", \"Bg\"],\n [\"Ag\", \"1Eg\", \"2Eg\", \"Bg\"],\n [\"Ag\", \"Bg\"],\n ],\n },\n\n D4: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [rAxis(AX_1_1_0, PI), rAxis(AX_1_N1_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"A2\", \"E\"],\n hmSymbol: \"422\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n C4v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [sx(0), sy(0)],\n 4: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"A1\", \"E\"],\n hmSymbol: \"4mm\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n D2d: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [sz(PI2), sz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1],\n A2: [1, 1, 1, -1, -1],\n B1: [1, 1, -1, 1, -1],\n B2: [1, 1, -1, -1, 1],\n E: [2, -2, 0, 0, 0],\n },\n raman: [\"A1\", \"B1\", \"B2\", \"E\"],\n infrared: [\"B2\", \"E\"],\n hmSymbol: \"-42m\",\n backscattering: [\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"E\", \"B1\"],\n [\"A1\", \"B1\", \"B2\"],\n ],\n },\n\n D4h: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(PI2), rz(-PI2)],\n 3: [rx(PI), ry(PI)],\n 4: [rAxis(AX_1_1_0, PI), rAxis(AX_1_N1_0, PI)],\n 5: [NI],\n 6: [sz(0)],\n 7: [sz(PI2), sz(-PI2)],\n 8: [sx(0), sy(0)],\n 9: [sAxis(AX_1_1_0, 0), sAxis(AX_1_N1_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n A2g: [1, 1, 1, -1, -1, 1, 1, 1, -1, -1],\n B1g: [1, 1, -1, 1, -1, 1, 1, -1, 1, -1],\n B2g: [1, 1, -1, -1, 1, 1, 1, -1, -1, 1],\n Eg: [2, -2, 0, 0, 0, 2, -2, 0, 0, 0],\n A1u: [1, 1, 1, 1, 1, -1, -1, -1, -1, -1],\n A2u: [1, 1, 1, -1, -1, -1, -1, -1, 1, 1],\n B1u: [1, 1, -1, 1, -1, -1, -1, 1, -1, 1],\n B2u: [1, 1, -1, -1, 1, -1, -1, 1, 1, -1],\n Eu: [2, -2, 0, 0, 0, -2, 2, 0, 0, 0],\n },\n raman: [\"A1g\", \"B1g\", \"B2g\", \"Eg\"],\n infrared: [\"A2u\", \"Eu\"],\n hmSymbol: \"4/mmm\",\n backscattering: [\n [\"A1g\", \"Eg\", \"B1g\"],\n [\"A1g\", \"Eg\", \"B1g\"],\n [\"A1g\", \"B1g\", \"B2g\"],\n ],\n },\n\n // =======================================================================\n // TRIGONAL\n // =======================================================================\n\n C3: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n },\n characterTable: {\n A: [1, 1, 1],\n \"1E\": [1, W2, W],\n \"2E\": [1, W, W2],\n },\n raman: [\"A\", \"1E\", \"2E\"],\n infrared: [\"A\", \"1E\", \"2E\"],\n hmSymbol: \"3\",\n backscattering: [\n [\"A\", \"1E\", \"2E\"],\n [\"A\", \"1E\", \"2E\"],\n [\"A\", \"1E\", \"2E\"],\n ],\n },\n\n C3i: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n 3: [NI],\n 4: [sz(NPI3)],\n 5: [sz(PI3)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1],\n \"1Eg\": [1, W2, W, 1, W2, W],\n \"2Eg\": [1, W, W2, 1, W, W2],\n Au: [1, 1, 1, -1, -1, -1],\n \"1Eu\": [1, W2, W, -1, [-W2[0], -W2[1]], [-W[0], -W[1]]],\n \"2Eu\": [1, W, W2, -1, [-W[0], -W[1]], [-W2[0], -W2[1]]],\n },\n raman: [\"Ag\", \"1Eg\", \"2Eg\"],\n infrared: [\"Au\", \"1Eu\", \"2Eu\"],\n hmSymbol: \"-3\",\n backscattering: [\n [\"Ag\", \"1Eg\", \"2Eg\"],\n [\"Ag\", \"1Eg\", \"2Eg\"],\n [\"Ag\", \"1Eg\", \"2Eg\"],\n ],\n },\n\n D3: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1],\n A2: [1, 1, -1],\n E: [2, -1, 0],\n },\n raman: [\"A1\", \"E\"],\n infrared: [\"A2\", \"E\"],\n hmSymbol: \"32\",\n backscattering: [\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n ],\n },\n\n C3v: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1],\n A2: [1, 1, -1],\n E: [2, -1, 0],\n },\n raman: [\"A1\", \"E\"],\n infrared: [\"A1\", \"E\"],\n hmSymbol: \"3m\",\n backscattering: [\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n [\"A1\", \"E\"],\n ],\n },\n\n D3d: {\n classes: {\n 0: [I],\n 1: [rz(TPI3), rz(NTPI3)],\n 2: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 3: [NI],\n 4: [sz(NPI3), sz(PI3)],\n 5: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1],\n A2g: [1, 1, -1, 1, 1, -1],\n Eg: [2, -1, 0, 2, -1, 0],\n A1u: [1, 1, 1, -1, -1, -1],\n A2u: [1, 1, -1, -1, -1, 1],\n Eu: [2, -1, 0, -2, 1, 0],\n },\n raman: [\"A1g\", \"Eg\"],\n infrared: [\"A2u\", \"Eu\"],\n hmSymbol: \"-3m\",\n backscattering: [\n [\"A1g\", \"Eg\"],\n [\"A1g\", \"Eg\"],\n [\"A1g\", \"Eg\"],\n ],\n },\n\n // =======================================================================\n // HEXAGONAL\n // =======================================================================\n\n C6: {\n classes: {\n 0: [I],\n 1: [rz(PI3)],\n 2: [rz(TPI3)],\n 3: [rz(PI)],\n 4: [rz(NTPI3)],\n 5: [rz(-PI3)],\n },\n characterTable: {\n A: [1, 1, 1, 1, 1, 1],\n B: [1, -1, 1, -1, 1, -1],\n \"1E2\": [1, W, W2, 1, W, W2],\n \"2E2\": [1, W2, W, 1, W2, W],\n \"1E1\": [1, [-W[0], -W[1]], W2, -1, W, [-W2[0], -W2[1]]],\n \"2E1\": [1, [-W2[0], -W2[1]], W, -1, W2, [-W[0], -W[1]]],\n },\n raman: [\"A\", \"1E2\", \"2E2\", \"1E1\", \"2E1\"],\n infrared: [\"A\", \"1E1\", \"2E1\"],\n hmSymbol: \"6\",\n backscattering: [\n [\"A\", \"1E1\", \"2E1\", \"1E2\", \"2E2\"],\n [\"A\", \"1E1\", \"2E1\", \"1E2\", \"2E2\"],\n [\"A\", \"1E2\", \"2E2\"],\n ],\n },\n\n C3h: {\n classes: {\n 0: [I],\n 1: [rz(TPI3)],\n 2: [rz(NTPI3)],\n 3: [sz(0)],\n 4: [sz(NTPI3)],\n 5: [sz(TPI3)],\n },\n characterTable: {\n \"A'\": [1, 1, 1, 1, 1, 1],\n \"A''\": [1, 1, 1, -1, -1, -1],\n \"2E'\": [1, W, W2, 1, W, W2],\n \"1E'\": [1, W2, W, 1, W2, W],\n \"2E''\": [1, W, W2, -1, [-W[0], -W[1]], [-W2[0], -W2[1]]],\n \"1E''\": [1, W2, W, -1, [-W2[0], -W2[1]], [-W[0], -W[1]]],\n },\n raman: [\"A'\", \"1E'\", \"2E'\", \"1E''\", \"2E''\"],\n infrared: [\"A''\", \"1E'\", \"2E'\"],\n hmSymbol: \"-6\",\n backscattering: [\n [\"A'\", \"1E''\", \"2E''\", \"1E'\", \"2E'\"],\n [\"A'\", \"1E''\", \"2E''\", \"1E'\", \"2E'\"],\n [\"A'\", \"1E'\", \"2E'\"],\n ],\n },\n\n C6h: {\n classes: {\n 0: [I],\n 1: [rz(PI3)],\n 2: [rz(TPI3)],\n 3: [rz(PI)],\n 4: [rz(NTPI3)],\n 5: [rz(-PI3)],\n 6: [NI],\n 7: [sz(NTPI3)],\n 8: [sz(-PI3)],\n 9: [sz(0)],\n 10: [sz(PI3)],\n 11: [sz(TPI3)],\n },\n characterTable: {\n Ag: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n Bg: [1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1],\n \"1E2g\": [1, W, W2, 1, W, W2, 1, W, W2, 1, W, W2],\n \"2E2g\": [1, W2, W, 1, W2, W, 1, W2, W, 1, W2, W],\n \"1E1g\": [\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n ],\n \"2E1g\": [\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n ],\n Au: [1, 1, 1, 1, 1, 1, -1, -1, -1, -1, -1, -1],\n Bu: [1, -1, 1, -1, 1, -1, -1, 1, -1, 1, -1, 1],\n \"1E2u\": [\n 1,\n W,\n W2,\n 1,\n W,\n W2,\n -1,\n [-W[0], -W[1]],\n [-W2[0], -W2[1]],\n -1,\n [-W[0], -W[1]],\n [-W2[0], -W2[1]],\n ],\n \"2E2u\": [\n 1,\n W2,\n W,\n 1,\n W2,\n W,\n -1,\n [-W2[0], -W2[1]],\n [-W[0], -W[1]],\n -1,\n [-W2[0], -W2[1]],\n [-W[0], -W[1]],\n ],\n \"1E1u\": [\n 1,\n [-W[0], -W[1]],\n W2,\n -1,\n W,\n [-W2[0], -W2[1]],\n -1,\n W,\n [-W2[0], -W2[1]],\n 1,\n [-W[0], -W[1]],\n W2,\n ],\n \"2E1u\": [\n 1,\n [-W2[0], -W2[1]],\n W,\n -1,\n W2,\n [-W[0], -W[1]],\n -1,\n W2,\n [-W[0], -W[1]],\n 1,\n [-W2[0], -W2[1]],\n W,\n ],\n },\n raman: [\"Ag\", \"1E2g\", \"2E2g\", \"1E1g\", \"2E1g\"],\n infrared: [\"Au\", \"1E1u\", \"2E1u\"],\n hmSymbol: \"6/m\",\n backscattering: [\n [\"Ag\", \"1E1g\", \"2E1g\", \"1E2g\", \"2E2g\"],\n [\"Ag\", \"1E1g\", \"2E1g\", \"1E2g\", \"2E2g\"],\n [\"Ag\", \"1E2g\", \"2E2g\"],\n ],\n },\n\n D6: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI3), rz(-PI3)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [ry(PI), rAxis(AX_SQ3_1_0, PI), rAxis(AX_SQ3_N1_0, PI)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1, 1],\n A2: [1, 1, 1, 1, -1, -1],\n B1: [1, -1, 1, -1, 1, -1],\n B2: [1, -1, 1, -1, -1, 1],\n E2: [2, 2, -1, -1, 0, 0],\n E1: [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1\", \"E1\", \"E2\"],\n infrared: [\"A2\", \"E1\"],\n hmSymbol: \"622\",\n backscattering: [\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E2\"],\n ],\n },\n\n C6v: {\n classes: {\n 0: [I],\n 1: [rz(PI)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI3), rz(-PI3)],\n 4: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n 5: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n A1: [1, 1, 1, 1, 1, 1],\n A2: [1, 1, 1, 1, -1, -1],\n B1: [1, -1, 1, -1, 1, -1],\n B2: [1, -1, 1, -1, -1, 1],\n E2: [2, 2, -1, -1, 0, 0],\n E1: [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1\", \"E1\", \"E2\"],\n infrared: [\"A1\", \"E1\"],\n hmSymbol: \"6mm\",\n backscattering: [\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E1\", \"E2\"],\n [\"A1\", \"E2\"],\n ],\n },\n\n D3h: {\n classes: {\n 0: [I],\n 1: [sz(0)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [sz(TPI3), sz(NTPI3)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n \"A1'\": [1, 1, 1, 1, 1, 1],\n \"A2'\": [1, 1, 1, 1, -1, -1],\n \"A1''\": [1, -1, 1, -1, 1, -1],\n \"A2''\": [1, -1, 1, -1, -1, 1],\n \"E'\": [2, 2, -1, -1, 0, 0],\n \"E''\": [2, -2, -1, 1, 0, 0],\n },\n raman: [\"A1'\", \"E'\", \"E''\"],\n infrared: [\"A2''\", \"E'\"],\n hmSymbol: \"-6m2\",\n backscattering: [\n [\"A1'\", \"E'\", \"E''\"],\n [\"A1'\", \"E'\", \"E''\"],\n [\"A1'\", \"E'\"],\n ],\n },\n\n D6h: {\n classes: {\n 0: [I],\n 1: [rz(PI3), rz(-PI3)],\n 2: [rz(TPI3), rz(NTPI3)],\n 3: [rz(PI)],\n 4: [rx(PI), rAxis(AX_N1_SQ3_0, PI), rAxis(AX_N1_NSQ3_0, PI)],\n 5: [ry(PI), rAxis(AX_SQ3_1_0, PI), rAxis(AX_SQ3_N1_0, PI)],\n 6: [NI],\n 7: [sz(TPI3), sz(NTPI3)],\n 8: [sz(PI3), sz(-PI3)],\n 9: [sz(0)],\n 10: [sx(0), sAxis(AX_N1_SQ3_0, 0), sAxis(AX_N1_NSQ3_0, 0)],\n 11: [sy(0), sAxis(AX_SQ3_1_0, 0), sAxis(AX_SQ3_N1_0, 0)],\n },\n characterTable: {\n A1g: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],\n A2g: [1, 1, 1, 1, -1, -1, 1, 1, 1, 1, -1, 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